Lelouch Lamperouge from Code Geass. I find him manipulative because he sort of sees the world like a giant chess board with him as the king. He's not a terrible person exactly but he does use people to get what he wants.
Takano Miyo from Higurashi No Naku Koro Ni [If you have seen Higurashi, you would hopefully understand] Bernkastel from Umineko No Naku Koro Ni [Same with Takano except she sees everything as a chess game just like Beatrice and Lambdadelta do.] -picture- Kyubey from Puella Magi Madoka Magica [His Looks are quite deceiving.] Legato Bluesummers from Trigun [Well, he has mind control. Knives is also pretty manipulative as well.]