Yeah, almost anything worth playing works well on it, and with a decent system the graphics options can make a lot of the 3d games not-horrible looking. I like the Dolphin emulator too; Wind Waker and a lot of Wii games look terrific with anti-aliasing and at higher resolutions.
There've been a good amount of decent NDS games over the last few years; Avalon Code, Dark Spire, the re-releases of the Dragon Quest games, that new Aliens game that's like a Metroid one, Fire Emblem anything, the FF: Tactics A2 is alright, the remade Lufia, Okamiden, Henry Hatsworth, Knights in the Nightmare (I think it's better on PSP), Rondo of Swords, and Black Sigil are just a few that pop to mind.