"Clutch quarterback" is not a formally defined term, but in common usage it refers to a quarterback who makes important positive plays for his team at key moments in games. (Those key moments are sometimes described as being "in the clutch.") This term is particularly descriptive if the games are important (i.e. playoffs, Super Bowl).
Some announcers use the term to describe a QB who has performed well just a few times. Personally, I would only use the term to describe a QB who has done this several times over a period of several years. Eli Manning made several great plays to lead his team to a come-from-behind win in the last Super Bowl, but in my opinion he hasn't done this often enough to deserve the title of "clutch quarterback." He has also made some very bad plays at key times in his career. Guys who do deserve the term in my opinion include Brett Favre, Peyton Manning, and - going back further in time - John Elway and Joe Montana. Being a "clutch quarterback" doesn't guarantee having a great performance at every key moment, but a clutch quarterback is someone who has a good chance of delivering a game-winning performance in a tight or important game.