Doodle Jump is fun, Fruit Ninja too, but sadly some of the best online multiplayer games aren't for Gamecenter
Modern Combat 2: Black Pegasus is a great FPS with online multiplayer through "Gameloft Live," Gameloft's gaming network. You are able to select "Join a Friend" on the multiplayer load-out to join a friend playing an online match already. ($6.99)
Real Racing 2, the newest in the Real Racing series also has great online play, which, luckily, is through game center! The smooth Gyroscope control make for a superior online racing experience. ($4.99)
Last but not least we have Archetype, a sci-fi combat game that is only focused on giving you a great multiplayer experience (meaning there is no single player campaign mode as the games above do include.) But for only 99 cents this game is definitely one worth checking out.