A Nintendo game always tops every attempt to make a best games list.
I've seen The Legend Of Zelda: Ocarina Of Time, The Legend Of Zelda: A Link To The Past, Super Mario Bros., Super Mario Bros. 3, Super Mario 64, and Super Metroid at the top of several lists that I can recall. Zelda games always crowd up the lists too, mostly deservably (I think Majora's Mask should usually be higher than it usually is, though).
On a related note, I hear Famitsu's only given perfect scores to five games, including Ocarina Of Time, Wind Waker, and the various Nintendogs games together. Sure, there's Soul Calibur (DC) and Vagrant Story (PSX) but Nintendo being the developer and the maker of the hardware that the game is on for three out of five is pretty good.
It really makes me wonder why there are Nintendo haters at all.
*high-fives all the Nintendo fans*