Brenda Leigh Johnson, The Closer
Deputy Chief Brenda Leigh Johnson played up her ditzy Southern belle persona like there was no tomorrow, practically elevating it to an art form. Many a suspect discovered far too late that this apparently absent-minded, chocolate-snacking bubblehead was actually a ruthless and brilliantly manipulative CIA-trained interrogator. "Thank you. Thank you *so* much!"
John Casey, Chuck
Maybe it's a bit of a cheat featuring Adam Baldwin twice, but John Casey was one of those characters who constantly surprised you. Described as a "burn-out" NSA agent early on, Casey appeared to be a gun-happy, none-too-bright, over-the-top patriotic bruiser. Over the course of the series, however, he was revealed to have perfect pitch (he was once a choir boy!), he could cook and plan a wedding, and his favorite movie was... Steel Magnolias.
Jack O'Neill, Stargate SG-1
Jack O'Neill at a cursory glance appeared amazingly obtuse and completely disinterested in anything even vaguely scientific. Then you realized that the man was (1) an amateur astronomer and (2) remarkably capable of applying in a practical manner the scientific techobabble his teammates had been spouting moments earlier! He was also a brilliant strategist and spoke reasonably fluent Spanish, and he was capable of figuring out and operating extraterrestrial spacecraft in a remarkably short amount of time.
John Crichton, Farscape
Whole empires have fallen after their leaders underestimated John Crichton. It's not surprising, though; after being sucked through a wormhole to a distant part of the galaxy, Crichton found himself in over his head and being endlessly pursued by unrelenting aliens who want to kill him or possess what he knows about wormholes. Because the guy who seemed utterly insane (he called his gun "Winona" and once had a coma-vision of Looney Tunes!) was actually a brilliant scientist and engineer -- he designed and built the space pod that got sucked through the wormhole. He also built a portable thermonuclear weapon once. Yep. Don't mess with John Crichton. Or anyone he knows. Ever.
Saul Goodman, Breaking Bad/Better Call Saul
Saul may come off like a sleezy, two-bit hack, the used-car salesman equivalent to a lawyer, but he was actually very, VERY good at what he does. And he also had numerous underworld connections that gave him a wide range of shady resources. At the same time, he was loyal to his clients and unafraid to give it to them straight. Saul knew enough, too, to wear a bullet-proof vest, showing he was not only smart, but prepared and well aware of what was likely to happen around his less-than-savory clientele.