Extended edition:
1996 - Super Mario 64 (runner up: Mario Kart 64)
1997 - Goldeneye (Diddy Kong Racing)
1998 - The Legend of Zelda: Ocarina of Time (Banjo-Kazooie)
1999 - Jet Force Gemini (Donkey Kong 64)
2000 - The Legend of Zelda: Majora's Mask (Banjo-tooie)
2001 - Halo:CE (Conker's Bad Fur Day/Luigi's Mansion) <--- What a fucking year!
2002 - Super Mario Sunshine (The Legend of Zelda: The Wind Waker/Star Fox Adventures)
2003 - F-Zero GX (Pokémon Ruby/Sapphire version)
2004 - Halo 2 (Metroid Prime 2: Echoes)
2005 - Mario Kart DS (Mario Party 7)
2006 - The Legend of Zelda: Twilight Princess (Wii Sports)
And my previously posted list (With runners-up added):
2007 - Halo 3 (Mario Party DS)
2008 - Super Smash Bros Brawl (Mario Kart Wii)
2009 - Halo Wars (Halo 3: ODST)
2010 - Metro 2033 (Halo: Reach)
2011 - Dead Space 2 (Battlefield 3)