Off the top of my head:
Starcraft & Starcraft: Brood War (has really good voice acting too)
Legend of Zelda: Majora's Mask - very cool that they took a series that had one of the most formulaic storylines of all and created something completely different for this game.
A lot of stuff in the point-and-click genre, like Day of the Tentacle, Beneath a Steel Sky, The Dig.







