I like cheese... oh, wait, that's not a Pokemon...
Umm... my three favorites are:
Celebi
Crobat
Pichu
As you can maybe tell, I'm a have-sex-with-Johto fan. I basically worship Gold, Silver, and Crystal.
There is one Pokemon from D/P that I like, and it'd be Togekiss, the third evolution of Togepi.