Ocarina of Time was ALTTP's story line with new graphics and put into a 3-D world. Difference is OoT was longer and harder to transverse worlds. Collect 3 pendants then collect 8 medallions in OoT and 8 diamonds for ALTTP. BTW, ALTTP is better on SNES than on GBA. While almost identical there are several changes inwhich I despise royally such as the addition of Like-Likes and the change of the mirror's sound. I do think that Ocarina of Time should of been on there, but it might of been limited to 1 game per series. And FF might be on there close to the top but the guy at PlanetGamecube said that GTA3 and Vice City were #s 2 & 3, which I find to be BS. These are just my feelings though and I do have to say that I have honestly played through ALTTP more than OoT. I've beaten OoT maybe 2-4 times and I've beaten ALTTP about 7-9 times, several of which include getting all the heart pieces. I beat it the weekend before I got WW. I sat down for a couple hours and I know the dungeons by heart so I breezed through it looking for difference of that and the GBA one. Beat the GBA one twice as well trying to get a different ending according to a FAQ. It didn't work. so overall between SNES and GBA, i've beaten ALTTP 9-11 times. (And I dont mean that as a joke, it just turned out that way while I was typing.)

EDIT: I also think that ALTTP coming out before OoT helped because it was really the first game that I ever got addicted to that I would sit down for long periods just playing it, and the first game I ever played through more than once.

EDIT:EDIT: / That doesn't count games like Mario for the NES where you always have to start at the beginning.