Pokemon Exclusive to Darkness: Mewtwo, Burmy, Buneary, Lopunny, Rotom
Pokemon Exclusive to Time: Celebi, Combee, Pachirisu, Riolu, Lucario
You can get wondermail codes that let version exclusive pokemon (except for Mewtwo and celebi, I think) join your team, and once you do that, you can find them in the wild.
You can find a list of version exclusive items here
. There may be some spoilers in that post, but the chapter summaries are under spoiler tags, so there shouldn't be much of a problem.