Greatest of all time? I'd have to go with The Legend of Zelda on the NES just because of how much it did all at once when compared to everything else at the time - all the way down to the gold cartridge, full color booklet with story elements and the map that it came with. I can understand people picking Super Mario Bros for the standards it set but I think Zelda's tight gameplay, level design of the overworld/dungeons and clever item usage will be timeless forever. And you got an entire second quest included right there on the cartridge that felt way more expansive than what SMB and other titles' second play-throughs gave you.
As far as "the best" 2D games of all time, you can add A Link to the Past (SNES), Super Mario World (SNES) and Castlevania: Symphony of the Night (PS) in there too.
