Thinking about it some more, Quake also holds up quite well I find, so much so that there's been a recent resurgence in the sort of simple fast paced old school shooter that it exemplifies.
A Link to the Past and Kirby's Dreamland 3 still look and play great to this day. Also, while I know some feel their prerendered graphics don't hold up, I personally feel the Donkey Kong Country trilogy are still fantastic.