Here's how to get good snaps of the following (in order of appearence):
Pidgey: Really not required because of the beginning, right?
Doduo: Hold the Z button at the beginning, then press A when he pops out.
Pikachu: There are MANY different ways:
The Surfboard: At the beach, lead him to his surfboard and take a shot.
The Stumps: When the first Meowth chasing a Pidgey appears, throw a pester ball at the Meowth when it sets foot on the track. You'll temporarily be stopped. Throw pester balls into that big bush. After Scyther appears, two Pikachus will walk onto the stumps. Play your flute, and after the second one (to shock) shocks, snap!
ElectRide: At the beginning of the tunnel level, snap Pikachu, then snap him again. When the Electrode hits him, he'll be rolling. SNAP!
Speed Demon Pikachu: If you throw an apple at the peeking Pikachu in the river, he'll get upset and run around acting like his tail is on fire.
On Balloons: In the caves, Pikachu is being carried by a Zubat. Pelt the Zubat, and Pikachu will get on balloons and fly away. SNAP.
On Articuno. Get Pikachu on balloons, and when Articuno flies out, Pikachu will be riding him. SNAP.
Scyther: Look at Pikachu at the stumps bonus (I mean on this, not the game.)
Magikarp: Any water. If you throw apples or pester balls into the water, occasionally, he pops up. In some places, he doesn't require throwing things.
Lapras: He's in the water at the Beach.
Kangaskhan: Throw a pester ball at him and he'll run up to you and yell "Kangas!" Snap him.
Pidgey gust bonus: If you let the two Pidgeys attack the Meowth, snap one of them when the whirlwind is showing.
Electrode: In the entrance to the Caves, they breed like rats.
Electabuzz: Snap the one running at the beginning.
Kakuna: They come down from the ceiling in the Caves. Note that if you wait, 4 will all come down at the same time. Snap.
Zubat: Snap them when they fly at you.
Haunter: Snap the purple flying balls.
Diglett: Get him when he's fighting Pikachu.
Dugtrio: Snap Diglett alot and it will turn into Dugtrio. After that, five will appear instead of three. Snap it again, and 2 Dugtrios pop out. Ultimate snap!
Magnemite: Throw an apple at one, then snap it.
Magneton: Hit all three with apples and they will link into Magneton.
Rapidash: Throw an apple into the pit by the Koffing volcano. The Rapidash will neigh. Snap.
Vulpix: Stun one with a pester ball so you can get close when it gets up. When you get close, snap when he looks near you.
Charmander: At the Vulpix egg, throw an apple by a Charmander it will call its friends. Do it to the other one, then lead them to you. Play the flute and snap them.
Moltres: Get Moltres flying in your direction to get more points.
Magmar: After the Moltres egg, throw an apple between the two Magmars. When they fight, snap them to get a bonus.
Growlithe and Arcanine: Throw Pester Balls into the pits across from the Charmeleon. If you get them shaking lava off, you get extra points.
Charmeleon: Just wait at the pit and snap.
Charizard: Knock the Charmeleon into the pit. It'll explode and evolve into Charizard. Throw an apple at him to make him spray flame. If you snap him then, you get extra points.
Poliwag: Throw Pester Balls at them to make them group up. Throw more and they'll dive in. If you snap two or three running in, you get more points.
Bulbasaur: Either knock one off the stump with a pester ball or lure one out by the first Bulbasaur stump with a hole in a log with an apple.
Shellder: They fly up everywhere.
Slowpoke: Snap it eating.
Slowbro: Lure a Slowpoke onto a muddy spot. It'll stick its tail in, get a Shellder caught on it, and evolve into Slowbro. Snap him.
Vileplume: Play your Flute when you see him. If you play different tunes, he'll dance differently. But, that's not really worth any bonus.
Psyduck: Throw food at the first one to sink it. If you throw food at the second one and a Psyduck pops out, take a picture for extra points.
Metapod: Throw a pester ball at one to lower it and get a closer shot.
Porygon: After you exit the Metapod tunnel, throw Pester Balls at the two moving spike type things in the wall by the exit. They'll pop out. If you throw another Pester Ball, they'll change to pink and blue. Move them together with apples to get more points.
Cloyster: He pops up into the air. Snap him.
Grimer: Get one to look at you, then snap it.
Ditto: Throw a pester ball at ANY Bulbasaur in the level.
Muk: Take pictures of the first two, then throw Pester Balls at the third. He'll evolve into Muk. I never found any way to get him to look at you.
Koffing: Snap one when you pelt one.
Jigglypuffs on Stage: (best with boosters) Hit all three Koffings chasing the Jigglypuffs. At the end, they'll be singing and dancing. You get more points for three than you do with two or one.
Weepinbell: Just snap the thing!
Victrebell: Knock Weepinbell into the little spring. Try to be really close when he evolves.
Jynx: After you play the flute, snap one. You get better when you snap the first one you see from under the egg. You automatically get a bonus for their dancing.
Articuno: He'll hatch from the egg where the Jynxs dance.
Squirtle: Hit one of the shells at the beginning with a pester ball. He'll get on land. If you snap him when he's coming out of his shell, you get extra points.
Dratini: Throw Pester Balls into the water, then snap him when he pops up.
Goldeen: Same as above, but Goldeen appears, too.
Gyarados: Try to knock a Magikarp at the Mankey by Mt. Dugtrio, and he'll hit it. It will land once you reach the Dancing Gravelers. Throw a Pester Ball at it to get it into the waterfall. Then it evolves into Gyarados. Snap it.
Geodude: Throw a Pester Ball at one on a wall, and it will fall, leaving you with a good picture.
Sandshrew: Snap one when a Geodude falls. You can get 2 or three together.
Sandslash: If you look at the thing that looks like Kadabra when you look to your left from the 3 Geodude wall, it's Sandslash. Get him while he's burrowing for a bonus.
Mankey: You can get a better snap from the one by the waterfall.
Staryu: He appears at the fast rapids. Snap him in the front.
Graveler: Play the flute by the 3 Gravelers on the wall and they'll dance for a bonus.
Starmie: When you snap Staryu in the front, go down the rapids, and at the whirlpool, he'll evolve into Starmie.
Dragonite: Throw 4 Pester Balls into the whirlpool and the big, retarded Dragonite will pop out. Snap him.
That's all, folks!