1. Ocarina of Time
Still the biggest pre-BotW Zelda ever made. It had something like 8 dungeons, and way more secrets than it's sequels.
2. Majora's Mask.
What can I say? Zelda has just aged well.
3. Final Fantasy 7 and all turn based RPGS. These didn't really have to grapple with 3D as much, since turned based combat doesn't need to solve as many development problems as other game modes.
4. Starfox 64
It's basically the last great Shmup IMO.
5. Super Mario 64
As long as you haven't been spoiled by the Galaxy series, or Odyssey this should still be good. Especially if you haven't played a 3D platformer since the PS2 days. It kind of starts off slow, and only really gets challenging once you open the 50 star door. But those later levels are still really good.
6. Final Fantasy Tactics
Alphamap graphics have a certain charm to them. Disgaea is on it's 5th game, because people like hand drawn alphamaps a lot! The gameplay also holds up well, thanks to being turn based, and not live action.