Many LocationsBasic rare pokemon:
1:1 Dialga/Palkia
1:2 Azelf
1:3 Uxie
1:4 Mesprit

Pokemon after national dex:
2:1 Rotom
2:2 Cresselia
2:3 Heatron
2:4 Giratina
2:5 Manaphy+Phione

Pokemon that require special events:
3:1 Arceus
3:2 Shaymin
3:3 Darkrai

Dialga and Palkia
The legendary dragons in pokemon diamond and pearl. This pokemon can be found at 
the top of mount coronet-sky pillar-. This pokemon can be found after team galactic 
has taken mesprit, uxie, and azelf. Once at sky pillar you have to take on the two 
galactic grunts. After their out of the way you must take on mars and Jupiter with 
your best friend or rival. After you kill them you have to take on Cyrus, the person in 
charge of team galactic, you may have remembered him from before and how easy he
 is. WellÂ… he toughened up big time. After deafeating him you may catch or kill Dialga 
or Palkia.They are at level 47.

Now that you have caught or defeated Dialga or Palkia you may catch Azelf. He is 
found in the middle of lake valor. He will be at level 50.

From this FAQ you may have caught Azelf first or moved on to Uxie or skiped this and 
moved to Mesprit. He can be found at Acurity Lake at level 50.

This may be the final lake pokemon to catch. Now before you go to lake variety go to
 the poketch place talk to the man and hell give you a poketch. Now fast forward time
 go back to him talk to him get a pokemon tracker poketch. Go to lake variety and go 
to mesprit. Mesprit will fly off. Track him down and have a strong pokemon who knows
 mean look. Then go for the catch.

This must be done at night. Go to the eternal forest and go to the old Chatue. Go up 
the stairs and go to the north door. Then their will be several doors. Search the rooms
 for a T.V. go to the T.V. and knock on it and Rotom will appear.

At Canclave City go to the house above the sailor. Talk to the boy who is spasing out.
 His mom will say something about a legend and to get some Lunar wing. Go to the 
sailor and he will take you to Fullmoon island. Go to Cresselia he will fligh of and leave
 the lunar wing. Take the wing back to the boy. Then do what you did for mesprit and
 catch Cresselia. She will be level 50.

Go to Fight area and you will meat some girl named buck. Go to Stark mountain and 
you will meat her again and team up with her. Take her to the treasure of the 
mountain. Go to survival area and to the house right next to the pokemon center. 
Buck will say something and leave. Go back to the spot where the treasure is. There 
will be heatron level 70.

On route 214 east of it will be a hidden lake that you need rock climb to get to. Once
 their go to the othere side and rock climb to the entrance. Go inside explore the the 
different entrances for a bit till you find Giratina level 70.

Manaphy can only be gotten from pokemon ranger. Once you have manaphy it cane 
be breaded. Its eggs will hatch after over 10,000 steps.  Its product will be Phiones. 
Phione can not be evolved.

This pokemon is open through Nintendo events that will be sent through Wi-Fi 
connection and is the god of all pokemon. In Japan this came out in July 2006. You will
 obtain the Azures flute. Go to sky pillar and use the flute and you will find arceus 
level 80. 

He is also aquired by Nintendo events. I am not sure where to find him but he is level 

This is what that little boy who helped you find cresselia was spazing about and he 
can only be acquired through Nintendo events. You will get a membrship pass and that
 hotel room you could never open in canclave is now open. Go on the bed and you will
 be in a place with Darkrai. When you see him he will be level 40.