Super Metroid. I would choose Ocarina, but its camera was annoying at times. Super Metroid had no flaws I can think of, it is the pinnacle of 2D gaming.
As to those people who think Metal Gear Solid 4 is the best game of all time. Listen to this: (lets see if I can embed it this time)
edit: screw it, here is the link: http://www.escapistmagazine.com/videos/view/zero-punctuation/99-Metal-Gear-Solid-4







