MGS3 (My favorite game of all time actually. Best pacing of any MGS game, best mechanics, best story, best bosses. Gameplay might have been refined in later games, but that's the only plus 4 and 5 have over 3 imo. The End and The Boss are the best 2 bosses in any game imo)
AC2 (Best pacing and level design in an AC game. Plus Ezio is really fucking cool, and the story is fun, without being too convoluted)
Pokemon Silver (Putting 2 Pokemon maps in one game is still insane to me, and hasn't been done in any other Pokemon game. Post game is so fucking good, with so much content. Nice variety of Pokemon as well, it's not too much of a grind, and the gyms are unique.)