I agree that a lot of 2d games have aged better than 3d games, since they suffer less from the graphics looking dated. The SNES/Genesis era is the most consistent, with most of the good titles from that era remaining good today. Same with GBA games. The NES is not as consistent to me since a lot of games seem more frustrating, thanks to a lack of saving combined with difficulty. Metroid, Mario 3, Legend of Zelda, Kirby's Adventure, and others are still fun. Nintendo titles in general tend to age well, actually. Even their N64 stuff has suffered less than most games from that era, especially Mario 64.
On the PS1, 2d sprite based games like Suikoden II and Castlevania: Symphony of the Night are amazing today. While I don't think FFVII has aged that well, FFIX and Chrono Cross are very playable today.
A lot of old PC strategy games and RPGs are still great now, too. HOMM 3 and Age of Mythology come to mind immediately, plus those classic Black Isle/Bioware RPGs. I've replayed KOTOR and Planescape recently and still found them to be a blast. Same with Fallout 2, which I played for the first time a couple years ago.