I guess it depends on what you mean by "looks best." Games that receive the iPad Retina update are the sharpest, most clear but that doesn't always mean a game's aesthetics look appealing.
Modern Combat 3 looks very nice. There are mods for GTA3 which make it look better as well. Real Racing 2 and Death Rally also look nice.
The Dark Knight Rises gets my vote for one of the finest looking games on the new iPad. For an open-world game to run smoothly at this level of detail is quite an achievement. Screenshots - http://www.candykiller.com/temp/TDKRscreens.jpg