...this can be applied to just about any work of fiction these days, but when you think of intelligent comic book characters you think of guys like Reed Richards, or Braniac, or Dr. Doom, or even Batman. They're not so much intelligent as they are just walking plot devises: if you have a problem, they can invent something that solves the problem or just come up with a solution after thinking real hard. With characters like these, science is pretty much the same as magic.

On the other hand, there are characters like Aizen from Bleach that are portrayed as extremely cunning but the context is hammy and feels extremely staged - they come off as always being two steps ahead because they're using a cheat sheet (how did they know so and so is going to do what in advance and that so and so will react, etc.)

Any characters out there that are believably smart instead of just magically smart?

Right now I can think of Elijah Snow and John Constantine. Their smarts don't seem so staged and particularly in Constantine's case, you get to feel that he's just reacting to stuff, instead of having some magical long-term plan that goes off without a hitch.