Often it describes a player who doesn't have overwhelming talent or scoring ability but who has a few elite tools and can change the way the game is played on either or both ends because of them.
Shawn Marion is a great example. I'd say Kawhi Leonard fits, too, and perhaps you could make a case for Tony Allen. Lamar Odom was an x-factor as well, though he fits the category of the inconsistent scorer, also. Battler was an x-factor for the Heat during their two recent championship runs. Boris Diaw is also an x-factor. Probably the biggest one in the playoffs this year.
The Spurs, honestly, derive a great deal of their success from an ability to make the most of those x-factor talents that other teams tend to misuse by casting them in too large a role or discarding them for more traditional players.