1. Captain America: Super Soldier
One of the best superhero games IMO. Arkham Asylum style combat may feel like a rip-off, but it works quite well for this game, resulting in extremely satisfying combat. Also, the game does a good job of making you feel like Captain America, with pretty well executed shield gameplay.
2. Dementium: The Ward
The best horror game you'll ever find on NDS. This game is one of the most horrifying games I've ever played, which is pretty impressive for a handheld game. Unfortunately, the combat and god-awful save system turns most people off. But I think the horror and atmosphere alone make this such a great game.
3. Resident Evil Remake
The best remake of anything ever made.
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This is war. Survival is your responsiblity.