Teebo from Ewoks is this throughout the first season, though he has moments in the second season as well. He listens to the trees, talks to animals, provides solutions to problems the gang is having and forms a closer bond with Logray, the village shaman.
Wade Load of Kim Possible, a ten-year-old super genius who invents all of Kim's gadgets. Oh, and, he's voiced by Taj Mowry, who also played the titular character of a TV show of the Trope Name.
Pickles the Drummer, of Metalocalypse, although compared to his bandmates that isn't saying much. Although all of the bandmates have at least one area of expertise despite being catastrophically stupid otherwise, Pickles is implied to be very intelligent: he can play several instruments (and started a highly successful glam rock band as a teenager), understand complex mathematics well enough to explain them to Nathan, read and write music, and seems to have graduated college despite champion-level alcoholism. He might even be a genius, except that because of his implied-to-be-supernatural tolerance, he takes drugs the way other people eat potato chips, and his miserable childhood left him with a level of emotional immaturity that generally puts him on par with the rest of Dethklok.
Twilight Sparkle takes the role in My Little Pony: Friendship Is Magic, though it's subverted more often than not due to her lack of real world experience to back up her vast book learning. She's certainly capable of some Awesomeness by Analysis however, along with some hardcore exposition.
Kyle from South Park often gets this role when compared with the others boys, and even Matt and Trey have called him the group's "smart kid".
Tako, the unofficial leader of the Sushi Pack, is the one usually called on to think of a plan to defeat the bad guys, and even has a standard "thinking routine". He also offers explanations of more complicated terms that come up in the show.
In Teenage Mutant Ninja Turtles 2003, Donatello's intelligence rises sharply to the point where he can build just about anything within a day or two (it seems to vary on how soon the team needs it), and figures out how to adapt Utrom tech, along with almost all other alien technology. He's also the guy with the Simple Staff, and generally considered the Technical Pacifist.
Blossom and Professor Utonium on The Powerpuff Girls both show some moxie in the intelligence department, but they will often get Flanderized (Blossom as egocentric, the Professor as a haplessly overconcerned parent) to keep them from being too one-dimensional.
Lisa Simpson in The Simpsons. Marge as well, in a few cases, but she is just a bit too oblivious to what constitutes as normal human behavior to do any discrediting.
In The Tick, the comics, animated and live-action series, the Tick's moth-garbed sidekick, Arthur, fills the role of the Smart Guy.
In Transformers Generation One, Wheeljack and Ratchet shared this role in the first season, Perceptor joined in as a third Smart Guy in the second season, and the third season saw Perceptor become the sole Smart Guy after Wheeljack and Ratchet's deaths in The Movie. The fourth "season" (really just a few episodes) introduced Brainstorm for this role, but the show ended before much could be done with him.
Winx Club made a half-hearted attempt to avert the "usually the technologically-minded character" aspect by having the girls mention that Musa and Flora get the best grades; nevertheless, the show kept using Tecna in the role of The Smart Girl. Timmy is also one for the Specialists, being the tech expert for them.
In the 4Kids version this turns a little racist; Flora's name is cut out of the best grades line, meaning that Musa, the Asian-inspired character, is the only one mentioned.
Walden from Wow! Wow! Wubbzy! fills this role on the show. As the theme song says, "he knows about science and books and art."