The 2002 Game of the Year is Metroid Prime.
The runner up is The Legend of Zelda: The Wind Waker.
The master thread for all of these contests can be found here.
There enough "Other" votes that there needs to be a Runoff Vote for 2002. There were three games from the original poll that had at least 10% of the vote, and there were three "Other" games from the comments that received at least two votes. First, here are the games from the original poll that made it to round 2:
Kingdom Hearts (PS2)
Disney meets Final Fantasy in this Squaresoft action RPG. This mash-up didn’t seem like it should work, but by the power Actraiser, they managed to make a fantastic game from this combo. This was also Tetsuya Nomura’s first time in a directorial position. This first entry would sell over 5.9 million copies on the PS2 and spawn a series that has sold over 36 million copies.
The Legend of Zelda: The Wind Waker (GameCube)
Sail the seas in cell-shaded graphics. This Toon Link adventure would sell over 4.4 million copies on the GameCube.
Metroid Prime (GameCube)
Metroid never got an N64 entry. However, many Nintendo fans were delighted to see Metroid become a FPS with this GameCube entry into the series. Metroid Prime scored a 97 on Metacritic and sold over 2.8 million copies on the GameCube making it the first Metroid game to outsell the NES original (which sold 2.7 million copies).
Here are the 3 games added from the comments:
Battlefield 1942 (PC)
This was the beginning of EA’s FPS franchise set during WWII. Battlefield 1942 sold over 3 million copies. The series as a whole has been played by over 50 million players.
Eternal Darkness: Sanity’s Requiem (GameCube)
Nintendo decided to publish their own take on the survival horror genre and was well received by the fans who played it. Eternal Darkness would score a 92 on Metacritic.
Resident Evil (REmake) (GameCube)
The first time a Resident Evil game was remade happened just 6 years after the original. REmake has more than just upgraded graphics, but also improved controls, extra content, a revised script, etc…. It is really a new take on the old game. This GameCube version sold over 1.3 million copies.
The Runoff Vote for 2002 Game of the Year will end on Thursday, Nov 2 at 11:59 PM, EST.
Games from the original poll that didn't make the cut:
The Elder Scrolls III: Morrowind (PC/XBox)
Warcraft III: Reign of Chaos (PC/Mac)
Grand Theft Auto: Vice City (PS2)
Super Mario Sunshine (GameCube)
Tom Clancy’s Splinter Cell (XBox)
Pokémon Ruby/Sapphire/Emerald (GBA)