Wow, I just noticed VG Chartz is in there!
Metal Gear Solid 4: Guns of the Patriots can obviously win this award easily, because there are a lot more gaming sites nowadays compared to the time when The Legend of Zelda: Ocarina of Time was released.
Actually, I think Ocarina of Time won "real" awards, not just GotY ones:
"In 1998, Ocarina of Time won the Grand Prize in the Interactive Art division at the Japan Media Arts Festival. It also won six honors at the 2nd Annual Interactive Achievement Awards, including "Game of the Year", "Outstanding Achievement in Interactive Design", "Outstanding Achievement in Software Engineering", "Console Game of the Year", "Console Adventure Game of the Year" and "Console RPG of the Year."