In this guide, I have split up what I believe to be the hardest bosses in Kingdom Hearts.  For the lesser of the hardest, I have made some short strategies.  For the top 5 or so(I didn't count), I have made in-depth strategies based off of multiple fights and experiments against the bosses themselves.

Bosses that are tough and/or annoying (I was killed 1-5 times against these bosses):
-Cloud (preliminary tournament)
-Cerberus (preliminary tournament)
-Leon & Yuffie
-Ursula, Flotsam & Jetsam
-Lock, Shock, and Barrel
-Oogie's Manor
-Captain Hook

-Maleficent
I will give some short strategies for these bosses, but not too detailed, for now at least.

Cloud: The easiest way to damage Cloud is to deflect his combo attack. When he yells "Ya!" and swings his sword three times. If you can deflect this attack, and pull off a successful counterattack, then you can deal a string of hits to him and hit him across the ring if you have the blitz ability. When he takes to the air and starts hitting you, dodge roll should be enough to keep you away from his attacks, if you use it at the right moment. The counterattack ability helps immensely in this battle.

Cerberus: Cerberus isn't too hard. You should pretty much try to string combos all the time with the exception of when he is about to spit dark matter into the ground. When they start biting you, stand on the outside and after they attack, go in for two or three hits. If you have high jump, you can sometimes get on top of Cerberus and avoid most of his attacks. This is useful if Donald and Goofy are dead and you need to revive them and do some healing.

Leon & Yuffie: You should take out Yuffie first, because she becomes more difficult if you defeat Leon before her. Deflect her weapons back at her and then hit her with a combo. When she creates her super disk, cast areo(ra)/(ga). If you corner her, string combos while she flips and throws things. Leon isn't too hard. When he yells "It's over!" and attacks, run behind him after he attacks and string a combo. Do the same thing when he charges up his gunblade.

Ursula, F & J: She isn't too hard. Just keep casting magic (preferably fire or thunder, but if you're using fire, stay further away, because it has to curve to get the right trajectory to hit the cauldron) at her cauldron until it "explodes", leaving her unconscious for a bit. String as many combos as you can during this time. When she's not unconscious, stay away from her, since you can't really hurt her now and her attacks can be a problem. If you need extra MP, defeat Flotsam or Jetsam. Each hit to them restores a bit of MP, and Ursula revives them every once in a while. When she revives them, she'll say "Get up and fight!”

Lock, Shock, and Barrel: For a bunch of kids, they are surprisingly tough. Cast aero IMMEDIATELY at the start. It will benefit you greatly. Take out whomever you please in whatever order. Watch out for Shock's spinning attack; it can be surprisingly deadly. This battle can get tough because it's sometimes hard to see them since they’re so small. Make good use of lock-on to help with this problem.

Oogie's Manor: First, make sure you destroy the orbs at the top of the manor first. Later, it becomes more difficult to scale the building, because there are more traps and the building becomes more and more violent the more orbs you destroy. Work your way down, and watch out for the flames the lantern emits. They get larger in numbers as you destroy more of the orbs. However, if you can deflect the flames, you'll get a handy 49 tech points for your effort.  If you get knocked off, go back up to the highest orb and start there again.

Captain Hook: Captain Hook is a pretty good swordsman, so watch out for some of his attacks. If you can deflect his attacks, this is the most ideal time to attack him. NEVER cast fire on him, because he'll just start running around in big circles while ascending into the air. So he'll probably hit you in this process a few times. It will probably give you problems at some point, so just don't do it. If you think making him fall into the ocean will work, don't get your hopes up, because he'll just jump back onto the ship and say "You'll not get me other hand!”(obviously talking to the gator).

Maleficent: At the start of the battle, bring the platform down by attacking it. Next, jump up and attack her from behind. If you hear her say "Meteors of heaven! Unleash your fury!" Get off the platform and run as far toward one of the side walls as you can. Because giant meteors will come out from behind her and strike anything within the diameter of the platform and anything in front of it. When she stops, go back up and chain combos again. She will likely use Dark Meteor again, so be ready. Repeat until dead.

Bosses that are insanely hard (I died 6+ times):
-Ursula (2nd time)
-Maleficent Dragon
-Riku II
-Phantom
-Kurt Zisa
-Sephiroth

I haven't gotten around to strategies yet for these bosses, but I'll have them up soon. Another thing is I haven't even beaten the game yet, on Ex. mode. I haven't tried yet. 

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Ursula (2nd time): Ursula is a lot harder this time, because she is so big, and she constantly turns to face Sora.  Since you can only inflict damage by hitting her head, the best way to attack is from the back.  Set cure and aero to Sora’s magic shortcut.  Have Ariel equipped with aero potion and cure potion, and Goofy equipped with MP gift, in your party. To avoid her bubble attack (which she announces by saying "Get ready for this"), use the mermaid kick to swim in a circular fashion away from your current position. When she starts to inhale water, use the mermaid kick to fight it. When you get behind and attack her, its best to cast aero to protect yourself. If you start to see a light appear above your head, move. This is a powerful attack, and the bolts constantly strike. When she starts to "teach you some manners" run away and let Ariel and Goofy start to weaken her. She will start to cast a circle of damaging magic around her, so you should avoid it, but Ariel should be able to keep the group going with cure potions.  A good opportunity to attack at this point is after she uses the attack where she shoots a beam of energy at you through her mouth.  Right after the attack, use the mermaid kick to get close and get a few hits in. After that, swim out again, because every time from now on when you get close to her face, she will use the attack.  Do this until she is dead.

Maleficent Dragon: This can be a frustrating fight. Set Sora's magic shortcut with curaga and aero. Have the beast and goofy in your party. Give them potions or high potions if you can afford them. Make sure Sora has the second chance ability. At the start of the battle, attack the dragon at its face, until it starts spewing fire.  When it does, get away until the fire cools down.  Keep attacking the dragon at its face. If you get hit, run away and heal. If beast and goofy die, jump on the dragon's back(you will need to jump on its hind legs or its tail to do this) and use potions on them.  One thing to watch out for is when the dragon will spin around and attack with its tail.  This attack is really annoying because you can’t really prepare for it, and you would need incredible reflexes to see this attack coming.  There isn’t really anything that announces it, so the only way you would be able to dodge it is if you happened to be on the dragons back and jumped right as it attacked by pure luck.  The key to winning this fight is patience and keeping a good eye on your health.

Riku II: This battle is probably the most strategy demanding and storyline-necessary fight in KH.  It is also very annoying to lose over and over because the cutscene right before the battle(you can't skip it) takes about 5 hours.  So to prepare, make sure Sora has dodge roll, second chance, blitz, and at least one combo plus equipped.  Also, set his magic shortcut with Curaga and Areora.  Lastly, fill all of Sora's slots with Hi-potions, and throw in an elixer or two if you want to.  At the start, wait until he does his short jump attack, and then attack him from behind. When he yells, "Heal this!" and does a jump attack, jump at him to avoid the shockwave, and hit him with an arial combo before you land. When you deplete his orange bar, he will gain a new attack. He will yell "Now witness true power!", then he will use an attack that resembles strike raid. The dodge roll ability is extremely helpful throughout the battle for avoiding this attack.  Even though you can deflect his keyblades back at him to cause damage, don’t.  It’s just a risk of your own health and it doesn’t cause that much damage anyway.  Keep your distance from him, because if you are close to him, it makes it easier for him to hit you with his attacks. At the end of this attack, he will jump up and strike the ground and some lightning bolts will strike down around you. He will then resume his original form. Proceed with the battle as you did before. This is not the only time he uses this however, he will likely use it again throughout the battle. When you eliminate his yellow bar, he will get yet another devastating attack. He will start glowing bright blue, then he will shoot back and forth across the ring. The best way to avoid this is to high jump and glide around until he settles down. If you get close to the ground, drop and immediately jump and glide again. At the end of this, he will float in the middle and lightning bolts will strike down all around you. It sounds bad, but it is avoidable. The best way to avoid it is to stay still if you aren't hit immediately, because if you keep moving, you might accidentally walk into one of the bolts.  If you continue attacking him the way you did at the start, and avoiding his two strong attacks, he should eventually die. I dodged his strongest attack 5 or 6 times before his green bar was depleted.

Phantom: Like Riku II, this is a very strategy demanding battle. It also takes a lot of preparation. First, have Peter Pan and Goofy in your party equipped with MP gift. Have Sora equipped with second chance. Give Goofy half ethers and half High potions. Do the same thing with Peter Pan. Fill all of Sora's slots with ethers.  Customize his magic shortcut with Curaga, Blizzaga, and either Areoga, Firaga, or Thundaga. 
Once you're ready.  Talk to Tink in the corner of the cabin to go to the clock tower. Phantom's weakness is the energy ball under him. When it is white, it can be damaged by physical attacks, when it is red, use firaga, for blue use blizzaga, and with yellow use thundaga. At the beginning of the battle IMMEDIATELY cast stopra on the clock tower (you have to get close to it) or phantom will sentence one of your characters to oblivion. Thundaga and blizzaga are easy spells to aim and cast on him. But use fire sparingly; if you try to hit him too much and miss, you can waste a lot of MP easily without noticing. Only use it when you have a definite and clear shot. When he stops in front of the clock tower, and casts a spell at you, hit it at the right time to deflect it, or it will get on you and cause damage. Every now and then, recast stopra on the clock, even if it hasn't worn off yet, if it starts up, it can eventually reach zero. Goofy will occasionally replenish your MP with MP gift. If he runs out of MP, give him an ether. NEVER USE ETHERS ON YOURSELF. For every 3 MP you give to Goofy, he can give 9 MP back to you. If you use your MP wisely and keep the clock stopped at all times, you should be able to win as long as Goofy doesn't run out of MP to give to you.

Kurt Zisa: This can be a pretty tough fight if you’re not at a really high level. It's best to be at least level 80-90 before taking Zisa on. To prepare for the fight, give Sora at least 3 mega potions, trust me, you'll need them, and the rest of his slots high potions. Also, customize his magic shortcut with areoga, curaga, and a third basic magic (fire, thunder, blizzard). High jump and dodge roll are essential in this fight. It also helps to have Ultima Weapon if you can get it. My recommendation would be blizzaga, I'll explain why later. Fill Goofy's and Donald’s slots with all high potions. Also, equip as many MP rages one everybody as possible, and equip MP gift on Goofy. That should keep your MP pretty high. At the start of the fight, immediately cast areoga on yourself, because Kurt will cast a spell to disable your magic for a while. He has two main attacks at this point in the fight. The first one is that he will start spinning his blades and rotate his body. The best way to avoid this attack is to run away until the attack ends, then when he is finished run back in to attack the orbs some. His second attack is that he will lunge forward at you and swing his blades at you. A sign that he is going to do this attack is he will jump across the arena, walk forward a bit until he gets closer to you, stop, then lunge at you. A good way to avoid this attack is to let him come toward you until he stops, and when he does, run out to the side to avoid the attack, then run back in to hit the orbs with some combos. These two attacks will alternate between each other until you destroy both orbs in his hands. Areoga assists greatly in this because it causes some extra damage to the orbs while you’re attacking them. When you destroy both orbs, Kurt will collapse in the sand for a short period of time. You must be ready as soon as you deal the final blow to the orbs. This attacking time is precious, you'll understand why later. The head bobs and weaves everywhere occasionally and is somewhat hard to hit. If you can deflect its attacks you'll get major tech points. You'll want to deplete at least 1.5 of his health bars in this period, to get an idea of what you need to do. Now, Zisa will change into a new form. He will form a protective barrier around him that can be only damaged by magic. The good news is that you have your magic back for the time being, so take advantage of being able to heal yourself with Curaga. He is somewhat hard to hit because he moves around a lot. The spell I would recommend using would be blizzaga, because if you can get close to him and hit him with all 7 parts of the scattershot, it will do a lot of damage.  Since it can deal so much damage in one shot, it is ideal because it doesn't cost much MP. As you attack the barrier, it releases MP balls. So pick them up often, as Donald and Goofy will ignore them and since he moves around a lot, the battle will be taken away from the MP balls and they will be wasted. As in his first form, he has two main attacks at this point in the fight. The first one is that he will make tornados appear around Sora and circle him. You can get out of them easily by using dodge roll. This is an ideal time to attack him with spells. His second attack is a little dangerous. He will make exploding energy balls appear in midair. They don't move, but if you touch them they will explode. The best way to avoid them is by either not moving and casting spells, or try to weave through them and avoid them to get to him. Keep an eye out because they are always appearing and you could easily run into an appearing one if you are escaping from another. Once the barrier's HP reaches zero, Kurt will collapse again. But you will have less time to attack him this time, so attacking time is even more precious this time around. Once back in his first form, immediately cast areoga like last time, as he will cast the magic-prohibiting spell again. Also this time, he will have a new attack. He will take flight, start spinning, and attack you like a swinging pendulum. There is a way to avoid this attack though. When he is spinning horizontally, use high jump to jump over him. When he is spinning vertically, use dodge roll to avoid him. Even though you can avoid these attacks, Donald and Goofy won't be so lucky. By now their high potions will most likely be depleted, and without magic, they're sitting ducks. Use a mega potion if Donald and Goofy get KO'ed. This is the most difficult part of the battle, so if you can get through this, you’re in good shape. If you don't manage to defeat him after you stun him this time, back in his second form, he also has a new attack. He will make energy balls travel through the ground like moles and come up under you to attack you. They should be pretty easy to avoid with dodge roll. By now you should be able to finish him off when you immobilize him this time. If not, the pattern continues until you do defeat him. Note that as the battle progresses, you have less time to attack him each time you immobilize him.

Sephiroth: For starters, this is a one on one battle between Sora and Sephiroth.  So you only need to prepare Sora for this one.  First, equip Sora with a Crystal Crown, a Gaia Bangle, and either an Omega Arts, or a second Crystal Crown (If you can spare the materials for one).  For his abilities, the essential ones to have are Second Chance (VITAL!), Dodge roll, Superglide, Ars Arcanum, Blitz (Important!), 2 MP Rages, and exactly one Combo Plus and Air Combo Plus.  You must only have ONE of each type of Combo Plus equipped, no more.  I’ll explain why later.  It really helps in this battle to have Ultima Weapon, and to be on at least level 90 or so.  You should also have all of the -ga spells.  For Sora’s magic shortcut, assign the spells Curaga and Areoga to the buttons of your liking.  The third spell doesn’t matter, because those are the only two spells that are essential in this battle.  For items, put at least 3 elixers in Sora’s slots, and fill the remaining slots with Hi-potions.

Now for the battle.  At the start, it shouldn’t be too hard.  He’ll walk around and attack you with his Masamune Blade.  He has two ways of attacking.  Either 1) He’ll stand still and swing his sword at you, or 2) He’ll lunge toward and away from you in an instant, attacking you at the same time.  The time to attack is during his first type of attack, when he’s standing still.  The trick to getting at him is to try to jump over his attack, and hit him with an aerial combo.  If you manage to get four hits on him (which is your max amount of hits per combo if you listened to my advice earlier), he’ll teleport a few feet away from you.  You’ll probably lose your auto-target on him during this time, but if you try to lock onto him after he teleports, you may be able to target him before he reappears, and hopefully either defect the attack, or avoid it.  This all happens in almost a second, so be on your toes.  With his second type of attack, don’t try to attack him, because it probably won’t work.  Just try to stay back or deflect the attack.  You can tell he’s going to do his first type of attack when he stops walking and stands till for a second.  You can tell he’s going to do his second type of attack if he bends his knees slightly after stopping.  Again, you don’t have much time to recognize this attack, so be ready for anything.  He also has a third attack you must always be on the lookout for.  In this attack he erupts three gigantic flame pillars around him.  If you get caught in them, try to get out as fast as possible.  If you’re on the ground at the time, use dodge roll.  If you’re in the air at the time, use superglide.  The time to expect this attack is hard to say, but in my experiences I’ve found that he usually does this attack after you start to attack him with a combo but fail to finish it.  The second situation I’ve found that he uses this attack is when he hasn’t used it for a while.  A good clue that a quarter second later he will use it is he will say “Power”, then use it.  If you don’t get caught in it, this is an ideal time to attack.  Wait just beside the flames until they disappear, then attack him while he’s vulnerable.  If at first his health meter isn’t decreasing at first, don’t worry.  He’s not invincible.  I’ve had the same problem more than once, and I have yet to find what causes this.  But it should eventually start decreasing like normal after a while.  After you deplete his first health bar, he will start moving faster.  He will run around the ring and use the same attacks as before, but faster, so attacking like last time isn’t always as easy.  However, you must watch out for one of his attacks.  First, he will be running around like normal, then he will teleport away and say “Descend Heartless Angel”.  It sounds like “Sin Harvest” (because Lance Bass sucks at speaking clearly); so don’t be confused by this.  When you know that he is using this spell, you must get to him as quickly as possible and hit him to stop the spell.  If you’re pretty far away from him, jump toward him and superglide to him.  Make sure you’re facing toward him when you use superglide, otherwise you could end up circling around him instead.  If you’re pretty close to him, you should still use superglide, but if you have a bit of time to spare, drop down in front of him so you can do a ground combo and hit him with Blitz on the last hit before he teleports to cause a little more damage.  But if you’re far away, its better just to hit him however you can and not risk it.  If you don’t make it to him, and he successfully casts this spell, all of your HP and MP will be depleted.  If you do not have Second Chance equipped, this will kill you.  If you do have it equipped, you will be left with 1 HP.  If you get affected with this spell, use an elixer as fast as possible.  Once you deplete his second health bar, He will use a new attack, and go into a flurry of slashes in an attempt to deplete your HP before you can heal.  At this point use Ars Arcanum to even the score.  So you should both be slashing away but no one is hitting anyone.  After this attack, he will go back to attacking like he did before, running around and slashing you.  Eventually, he should use an attack where he will start glowing blue, and go to the center of the ring.  He will then make huge oval like rocks fall from the sky and stand in place.  The rocks will then start rotating around the ring.  Try to weave between them to avoid getting hit, because they cause damage when they hit you.  While this is going on, Sephiroth will be gathering a massive ball of energy above his head.  When it gets big enough, the rocks will disappear and he will throw the ball of energy at you.  As far as I know there is no way to dodge this attack, because he will always turn to face you right before he throws the ball.  This part of the battle is pretty hard to keep your health up, so when in doubt, use Curaga to bring your health back up.  When you get to his last health bar, he will attempt to finish you off.  He will have a new attack where he turns blue and does an attack, which is so complicated I can’t explain it very well.  It sort of looks like a flip and a sword slash to me, and you know he will use the attack when he says, “Dodge this!”  At this point, you may want to cast Areoga to help keep your health up.  Attack whenever you get the chance to, because there isn’t really an ideal time to attack during this part of the fight.  He may use any of the attacks he used previously in the fight, so be prepared for anything.  The important thing here is not to let your guard down, because if you do, it could easily cost you the fight.