I'll rank them.
1996: Super Mario 64 (this one's easy)
1997: Riven: The Sequel to Myst
1998: Ocarina of Time
1999: Harvest Moon 64
2000: Skies of Arcadia (also the year of Shenmue, so this is a close one)
2001: Tony Hawk 3
2002: Morrowind (another easy one!)
2003: The Wind Waker
2004: Tales of...