Mao (Disgaea 3). An Overlord tier demon with an EQ (Evil Quotient) of 1.8Million. He's an actual mad scientist.
Obliterates the universe in a bad ending tooTomoyo (Clannad). Very smart, and freakishly powerful (juggling opponents in the air Chun-Li style is EZ for her).
Kazami Yuuji (Grisaia series). Far stronger and resilient then he looks. On one hand, can single handedly slaughter a bunch of hardened terrorists. On the other hand, devises some interesting plans to help his female friends move beyond their psychological problems.
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This has been another (probably) uselessly informative post, by me. Booyah!
http://www.youtube.com/user/MrEvilbyte