EarthBound Beginnings was robbed, I tell you! ROBBED!
Well, okay, not quite. Sure, the digital release of Metroid Prime Trilogy wasn't quite as groundbreaking, but when it comes down to quality, it's no small feat topping those titles. Additionally, it's not easy tracking down the original Wii copy. It's a fair win.
Quite a few N64 games made the list, too. I've been getting nostalgic for that system lately...if only my old cartridges weren't contaminated with graphical glitches, and if only Nintendo stopped applying that nasty dark filter to their VC games. Please take care of your games, everyone!