In Kingdom Hearts, Donald Duck is The Smart Guy of the team, being the Disney Court's royal magician, and good at his craft. However, he doubles as the bad kind of team Lancer as well, because of how self-centered, small-minded, and short-tempered he is; he's always trying to get his way, and doesn't consider the consequences of his bullish behavior. All of the wisdom is instead found in Goofy, The Big Guy of the team, making him something of a Genius Bruiser. This pretty solidly seems a case of Dumb Is Good. Actually, considering how many evil scientists there are in the series, it could seen as a double-whammy of Dumb Is Good and Science Is Bad. Even good-guy inventor Cid can't escape the fact that his gummi ships couldn't be built without breaking off material from the shells that protect each world from Darkness. Goofy's also the only one of the trio that knows how to properly use a computer (Sora only barely knew how to type and Donald had no idea) as well as caught on to Mulan's true nature.
Persona 4 has a few possible. Early in the game, the Lancer Yosuke doubles as this, as the only guy with any plausible investigative theories. Yukiko might also qualify. Later in the game, Yosuke relinquishes this post for Ms. Exposition Naoto.
The Engineer, Medic, and Spy of Team Fortress 2 all fit the role. The first is a relatively goodhearted Gadgeteer Genius, the second is a crazy Mad Scientist, and the third is a haughty Magnificent Bastard. All utilize technology, and they neatly encapsulate all traditional Smart Guy skills — machines, support, and subterfuge. And all of them are arguably Bat-Shit Insane.
Siblings Welkin and Isara Gunther from Valkyria Chronicles usually fill out the role of being smart for Squad 7. Coincidentally, they're both in the tank.
Mass Effect 2 has Mordin Solus, who is an Omnidisciplinary Scientist (mostly) who runs the technology lab. Tali returns, still an engineer and tech expert. Legion, an Automaton, possesses the collective technological knowledge of the Geth, and Kasumi Goto is the greatest hacker and infiltration specialist in the galaxy.
Mass Effect 3 has Tali, once again, and EDI, the crew's Do Anything AI. Liara, as the Shadow Broker, has shades of it as well, with her research on the Protheans coming in handy once more and leading not only to the discovery of The Crucible, kicking off most of the plot, but also uncovers Javik, the last Prothean.
Halo: The Huragok serve as The Smart Species. They're the only ones in the Covenant who actually know enough about their technology to build and maintain it, which puts the other races in a bind when most of them vanish after the third game.
Cortana also acts as a smart girl for the Master Chief.
Damon Baird is the smart guy for Delta Squad in Gears of War.
In Final Fantasy VIII, Quistis Trepe fulfills this role because she is initially their teacher. Selphie Tilmitt might also fit because of her knowledge of weaponry and explosives.
But then, even Zell could work, because he's quite knowledgeable on the history of a few places the SeeDs visit, and occasionally serves as exposition before missions.
Final Fantasy XIII gives us Hope Estheim, the youngest of the cast but with the highest magic stat.
Lester from Grand Theft Auto V. He's crippled and requires a cane or wheelchair to get around, but he comes up with the plan for almost every major heist and sets up assassinations (as well as mentioning how to use the assassinations to manipulate the stock market).