Alphas: Gary Bell is a high functioning autistic twenty-year old with transductive powers.
The A-Team: Face filled this role as the scroungingCon Man who always had a financial scheme up his sleeve. There are episodes where he geeks out over the intricacies of his latest con, and he was shown to be great with doing math in his head quickly. Ironically, Face was also the team's handsomewomanizer.
Agents of S.H.I.E.L.D.: Both halves of "Fitzsimmons": Leo does the physics and engineering stuff, Jemma has two PhDs and handles biochem.
Barney Miller: Dietrich was a master of low-key wit and arcane knowledge, tossed off in a kind of humblebraggy way.
Bones: Also plenty to go around. Brennan often fills the role, but Hodgins or Zack have as well, or one of the rotating 'squinterns'.
Skyler uses an off-hand remark about having two phones to figure out that Walt is a drug dealer, convinces the IRS that fraudulent accounting by a former friend was due to incompetence on her behalf and spins a story about Walt having a gambling problem.
Saul, meanwhile, portrays the images of a sleazy lawyer but is in fact highly competent, convincing Walt and Jesse to set up a drug empire and helping Skyler obtain a carwash to help launder said drug empire money through.
Had Giles, and the spinoff Angel had Wesley. Watchers are pretty much Smart Guy incarnate. Angel also had Fred, a mixture of the Smart Guy/Hot Scientist and The Chick. In addition, Anya could be considered a Smart Guy when talking about demonic matters (with which she has personal experience), although less so in most other matters (such as "how to conduct myself in human society"). Willow was also very smart, as well as magical. Giles was better educated but functioned more as their mentor, whereas Willow was clever/good with computers.
Between Seasons 6 and 7 Dawn had taken on this role, along with a bit of Wrong Genre Savvy.
Gunn got in on the Smart Guy role mixed with a bit of Smartass Guy in season 5 of Angel, after his brain upgrade.
Criminal Minds: Dr. Spencer Reid fits this to a T. Although, ironically, he's the tallest person in the cast.
Chuck: Stephen and Ellie both fit. Stephen's work made for the entire plot of the series and Ellie - PhD, MD - is one of the only people that can understand said work.
Everyone on all the shows in this franchise is smart, but each has a stand-out one or two:
CSI: Gil Grissom and Ray Langston. Now DB Russell is getting in on it too.
Some of his companions fulfill this trope, too, most notably his granddaughter, Susan, Zoe Heriot, Romana (who might be smarter than the Doctor himself), allegedly Adric, and Martha.
Dollhouse: Although many of the workers in are intelligent, Topher is the one who best fits this trope.
Glee: At first it looked like Artie would be The Smart Guy for the show's New Directions, but lately the role has started to shift over to organiser extraordinaire (see: 'Le Jazz Hot', Burt and Carole's wedding, the 'Barbra Streisand' flash mob) and genuinely bright kid Kurt Hummel.
Lost: Sayid Jarrah is an expert in communications technology. In his time on the Island, he has built several radios and fixed a computer. Physicist Daniel Faraday also counts, besides his amnesia and moments where he isn't much clear while explaining. It's also taken Up to Eleven in season four when he takes a look at a chopper and states that it can fly and even more when he dismantle an H-Bomb, taking its core, later in season five.
Also Gaius, who is not as powerful as Merlin, but knows a lot about magic. He is also the the court physician and teaches Merlin about medicine.
NCIS: On Team Gibbs, Tim is at the top of the list, though neither Ducky nor Abby are slouches.
Noah's Arc: Chance fits this role, being a college professor continually in pursuit of his academics. He also is a bit more withdrawn compared with the rest of the cast, and often will explain more complex matters to the rest of the group (often doubling as Mr. Exposition in the process). Though he doesn't wear them often, hes also the only one of the main cast who wears glasses, and is fairly thin compared to the more muscular (and in Alex's case, thicker) cast members.
Billy Cranston was the first PR smart guy, and it's hard to find one since who's embodied the trope as much as him. He invented their communicators, built a Flying Car and a body-swap machine in his spare time, and was a near-constant lifesaver when it came to fixing out-of-control Zords or teleporting into other dimensions.
Trip from Time Force is also a good example. Cam from Ninja Storm started out as this before getting the Sixth Ranger suit. When pulling double-duty proved exhausting, he came up with the unique solution of making a Projected Man version of himself to pick up the slack.
T.J. from Power Rangers in Space is another example. He's managed to save the team with a well-thought out strategy on more than one occasion, including against the Psycho Rangers.
Pretty Little Liars: Spencer and Aria both fit the bill, depending on the situation. Mona is the villain version of this for the A team.
Revolution: Aaron Pittman and Maggie Foster share the role in "Pilot", "Chained Heat", and "No Quarter". Aaron is quite knowledgeable about electronics, which is a skill rendered almost obsolete in the wake of a 15-year-long worldwide blackout. Maggie is quite knowledgeable about medicine in general. However, once Maggie dies in "The Plague Dogs", Aaron becomes the one Smart Guy on Team Matheson. After "Nobody's Fault But Mine", Rachel Matheson becomes a contender for this trope.
McKay is probably the most egregious example on modern TV; often, the other characters will just sit around and threaten him until he comes up with a plan.
Samantha Carter is more Badass Bookworm than just The Smart Guy; Zelenka is McKay's much more reserved and polite second in command. The remaining scientists tend to fit a different trope, in no small part as they are not members of the Five-Man Band.
Stargate SG-1: Samantha Carter and Daniel Jackson share the role of The Smart Guy. They do have their own specialties, however, with Samantha Carter being the technology expert/astrophysicist and Daniel Jackson being the archaeologist/anthropologist/linguist. Both of them can be considered Badass Bookworms.
Data. Given that he's an android, with a super computer in his head, he can usually come up with solutions that would be at best impractical if they didn't have an android on the crew.
Geordi LaForge and Dr. Crusher both have elements of this as well. As the ship's chief engineer, Geordi is the resident Gadgeteer Genius and the one who usually repairs Data. Dr. Crusher is obviously The Medic and is also the mother of Wesley.
Wesley plays with this one; although he's smart and the equal of at least the junior crewmembers on a technical basis, he lacks the credibility (partly due to his young age) to get the people with real power to listen to him. Usually Data will listen to him (because Data is only evaluating Wesley's evidence on its face alone) but occasionally Geordi, Riker, or Picard will be convinced—but never Worf.
Star Trek: Voyager: Does not have one clear cut Smart Guy, but several members of the crew display various aspects of it. Tuvok is a Vulcan and therefore is naturally The Spock. B'Elanna Torres is the chief engineer and therefore the most tech savvy. The Doctor is obviously The Medic and, like Data, his "brain" is a literal supercomputer. Finally, as a former Borg drone, Seven of Nine has access to the combined knowledge of every alien race that the Borg have ever assimilated.
Top Gear: James May, whose interest in detail and facts borders on obsession and alternately amuses and bores his non-scholarly co-presenters.
Torchwood: Ianto Jones and Toshiko Sato both fit this.
Vikings: Due to his upbringing as a Catholic monk, Athelstan is the most well-educated character on the show. Unlike the Vikings, he can read and write multiple languages as well as speak them, spent time in Charlemagne's court, and displays a great deal of knowledge on cultures and religions outside of his own, including Ancient Rome and its predecessors. By the time of Athelstan's capture in Wessex, he has also become the foremost expert of Saxon blood on the Norsemen, their culture, and paganism in general.
The West Wing: No one of the regulars was shown as unintelligent, but Toby was the only one who's intellect was regularly shown to rival that of President Bartlett.