I'd have a big list since I watch too much anime, but I'll try and make the list as small as I can.
Lelouch Lamperouge (Code Geass) - One of the most intelligent characters in the history of anime.
Light Yagami (Death Note) - Another intelligent character, same ending like Lelouch.
Kamina (Gurren Lagann) - Biggest rolemodel for any guy. He's on a level far beyond everyone else!
Zaraki Kenpachi (Bleach) - What can I say about this guy? Brute force, takes slashes, and keeps going like nothing happened.
Edward Elric (Fullmetal Alchemist) - Smart, cool, and short.
Takizawa Akira (Eden of the East) - Another very intelligent character, who also has the
Black Star (Soul Eater) - The assassin who will surpass god, enough said!
Orihara Izaya (Durarara!!) - Pretty creepy character, the "informant", and has a pretty messed up head.
Isayama Yomi (Ga-Rei Zero) - She was a really beautiful character, strong, loving, and an unexpected fate.
Yeah.. the girls don't get much leading roles in the animes I watch.. sorry lol.