We know and love him. His shows & movies are high quality geeknip: the wry genius who tolerates the plodding intellects of his companions just long enough to solve their problems. He's that lovable Übermensch whose just-this-side-of-functional people skills make him hard to like but fun to cheer on. Case studies: Sherlock, House, Tony Stark, Dr. Who. See Insufferable Genius on the ever-beguiling site TVTropes.
Charlie Jane Anders makes a reasonable case against him in Why I'm Kind of Tired of the Smartest Man in the Room.
The "smartest man in the room" is a kind of wish-fulfillment for reasonably smart people, because he's not just clever but incredibly glib.
…[T]his stereotype — like all stereotypes — is comforting. It's comforting to people who see themselves as "smart guys," because these dudes are basically perfect except for a few brilliant flaws. But it's also comforting to everyone else, because it confirms our basic sense that people who are smarter than us are messed-up individuals, who can't communicate with other people and who are missing some basic element of humanity.
The article doesn't try to make the case that the smart-guy icon necessarily is a corrosive one - more that it's growing a bit shopworn, and affecting the quality of storytelling.
…[T]he real problem is, "Smartest Guy in the Room" has become a genre, with its own tropes — and the story has to be distorted so that everybody else can be dumb enough to let the Smartest Guy be really smart.
This article acknowledges the fact that The Smartest Guy is always just that - a guy, but doesn't go too far down that rabbit hole. One wonders how audiences would react to a female character who ran intellectual rings around her companions and was unashamed to point this out with the same zesty, belittling insults we enjoy from the men.
What's funny about this piece is that the smart-guy characters are so well designed, as if crafted to appeal to us, that the author can at best muster up only a lukewarm dislike for them.