I know I'm gonna get some flak for this, but I think there needs to be two separate categories for 'best game ever' games in 3-D, and games not in 3-D.
Like how do we compare the graphics, controls, etc. of these games:
Contra
Super Castlevania IV
Versus this:
Shadow of the Colossus
Kind of a big difference in graphics right?
By the way, I think all of these games are A+ grade, and I love all of them.