Metroid Prime has to be pretty far up there. It was a bold step forward for an established franchise that could have gone wrong so many different ways, but holy cow they nailed it. The controls are probably the only weak part, but to be fair dual analog controls hadn't really caught on yet. Every area of the map has character. So many of the boss fights are memorable, from Omega Pirate being fueled by raw Phazon and destroying its own soldiers, to Thardus whiting out the whole arena, to Meta Ridley wrecking the shit out of the Artifact Temple. The music is great, bringing back bangers from previous games, subtly remixing in other motifs from the past as well to give the game a familiar feeling, while adding beautiful new ambient music of it's own. The plot progresses forward with only a limited amount of cut scenes and dialog. It combined two genres in an innovative new way that 20+ years later still hasn't really been recreated yet.

And then once you've finished playing everything and finding every last thing as intended, there's still more fun to be had in learning some of the more basic glitches to get items way earlier than intended. Giving the devs the middle finger by getting items the first time around without taking a long backtracking trip later to come back and get it. Speeding through areas and blasting through boss fights with equipment and weapons you're not supposed to have yet. It contributed in large part to the birth of the modern speedrunning scene as people came up with more and more creative ways to get around formerly impassable obstacles.

20+ years old now, and it still holds up (as long as you play Primehack or Remastered to get more modern controls).