Far Cry 2
This one's in because of its heavy use of wooded areas, which really do look great in 3D. It's also a game that looks leagues better on the PC than it does on consoles. The more generic town areas don't look nearly as nice, and the game as a whole can be quite frustrating, but Far Cry 2 is worth playing for the trees alone.
This might seem like an odd choice, but StarCraft II looks great in 3D. We're going to stop short of saying "it's like a table-top game come to life" as has been said online, but the Blizzard RTS shows that it's not just action games that benefit from 3D technology.