Smart Cartoon Characters

Well, in all the animated adaptations, Reed Richards of the Fantastic Four is the brains of the outfit, to the point that Reed Richards Is Useless. His arch-nemesis, Doctor Doom, qualifies as well.

Professor Phineas J. Whoopee is the go-to guy when Tennessee Tuxedo and Chumly need answers.

Valerie Brown is the Gadgeteer Genius among Josie And The Pussycats, in that she can MacGyver many solutions to the 'Cats dilemmas.

Though both Jake Clawson and Chance Furlong, a/k/a the SWAT Kats, are top-notch mechanics, Jake seems to be the more inventive of the two. Chance, however, is the better pilot.

There's also Merilee from "Butch Cassidy And The Sundance Kids." Her disguises always work, and she accompanies Butch more often than the others. Then there's Princess Ariel, who's always explaining things to Thundarr, like when he mistakes a movie poster for a marker. Finally, we have Velma Dinkley, who not only pieces together the clues, but is multilingual, and also brilliant enough to become a NASA scientist.

Double D AKA Edd from Ed Edd 'N Eddy was the brains behind putting together Eddy's harebrained scams .

Dotty, the youngest member of the Clue Club. It was she who found clues via online background checks, long before that became a common practice! Makes you wonder why the others refused to let her join them in their investigations.

^ Same reason one does not put military strategists on the front lines: the campaign goes so much better when those who can figure out how to defeat the enemy aren't getting riddled with holes. Dottie is too valuable to be put in harm's way. Plus, how exactly could she do her online research when laptops and wi-fi hadn't been invented yet?

Oh, and let us not neglect Lex Luthor. Inventor, entrepreneur, strategist, criminal mastermind ... this guy engineered his way into the Oval Office, so he's clearly thinkier than Superman.

Well, she did have a home computer at her disposal. It could even talk.

Simon Seville
Alvin and the Chipmunks

Simon and Theodore often find themselves following Alvin's lead but Simon Seville is the smartest of the brothers.
Simon often shows a measure of caution when entering Alvin's many schemes.
Alvin ignores his advice of course, but when the plan falls apart it's Simon who thinks their way out of trouble.

Dexter
Dexter's Laboratory

I'm a little surprised no one's mentioned Dexter yet. The series is all about a young prodigy's love of science.
Although many episodes show that he's often more intellect than common sense.