Mario, punch out, old nintendo games are pretty much mostly wonderful, etc. FF7 with mods to gameplay and graphics. Deus Ex with Mods to graphics. A lot of PC games with mods to graphics and gameplay.
The thing with a lot of older games, is that while some of the gameplay ideas are more complex and better (compare Deus Ex to Deus Ex HR). The level design, ways to break into things, and ways to do things is better in the older games. The gunplay, and stealth and level size has advanced a lot since then and HR far surpasses it in that area. Mario 64 has things that no other platformers have. But, it has a terrible camera and things that have been vastly improved since. That said I still like the first Deus Ex and Mario 64 more than the newer ones. But, I could definetely understand why someone would like the newer ones better. This applies to more games than just those as well.
A lot of RPG's west or eastern have better and more fluid combat systems, but a lot of times it comes with other dumb-downed mechanics compared to games of the past.
2D Sprite based games have aged the best (Megaman, Castlevania, Metroid, Mario), because in my mind they weren't near as limited by technology at the time to make the game the desired.
