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)

Here are some other notable games from the year 2002:

DDRMAX2 (Arcade)
Soulcalibur 2 (Arcade)
Battlefield 1942 (PC)
Final Fantasy XI (PC/PS2)
Freedom Force (PC)
Heroes of Might and Magic 4 (PC)
Icewind Dale 2 (PC)
Mafia (PC)
Medieval: Total War (PC)
Neverwinter Nights (PC)
No One Lives Forever 2 (PC)
Rollercoaster Tycoon 2 (PC)
Tigar Woods PGA Tour 2003 (PC/Xbox/PS2/GameCube)
The Getaway (PS2)
The Lord of the Rings: The Two Towers (PS2/XBox/GameCube/GBA)
Medal of Honor: Frontline (PS2/XBox/GameCube)
Ratchet and Clank (PS2)
Spider-Man (PS2/XBox/GameCube/GBA/PC)
SOCOM U.S. Navy SEALs (PS2)
Tony Hawk’s Pro Skater 4 (PS1/PS2/Xbox/GameCube/GBA)
Eternal Darkness: Sanity’s Requiem (GameCube)
Resident Evil Zero (GameCube)
Resident Evil (Remake) (GameCube)
Starfox Adventures (GameCube)
Golden Sun: The Lost Age (GBA)
Kirby: Nightmare in Dreamland (GBA)
The Legend of Zelda: Four Swords (GBA)
Metroid Fusion (GBA)

Feels good to cast the first vote. Warcraft III at 100 % as it should be!
But seriously though this is the first of two extremely easy choices for me, Warcraft III is my most played game ever and one my absolute favorites to this day. There were other great games this year tho so my top 5 would be:

1. Warcraft III
2. Pokémon Ruby and Sapphire
3. Wind Waker
4. Golden Sun: The Lost Age
5. REmake

Metroid Prime, for me. Not only a perfect transition into 3D for the beloved series, but a phenomenal action-adventure game dripping in atmosphere, surrounded by excellent music and sound design, and propped up with engaging, methodical gameplay focused on shooting and exploration.

Oh, 2002. It's one of those years for me.

Plethora of really great games: Wind Waker, Warcaft III: Mafia, GTA Vice City, Metroid Prime, Ratchet and Clank

Crapload of great PC RPGs:
Gothic II - Gothic, but bigger and better
Morrowind - for many still the best Elder Scrolls (though Daggerfall fans would probably disagree)
Neverwinter Nights - Bioware's first 3D DnD game, based on 3e ruleset
Arx Fatalis - first Arcane's game, heavily influenced by Ultima Underworld, with fun "draw with mouse" magic system
Dungeon Siege - action RPG, but with actual party and skills that upgrade as you use them

But in the end, for me, it comes down to choosing something that did something quite different - Battlefield 1942. It was team-based, WWII FPS on large maps, all with infantry, tanks, artillery and planes, 32vs32, which was massive at the time, with AI bots for training and focus on online (or LAN) multiplayer. Sure, WWII Online came a year before that, it was the first MMOFPS, and it simulated West European WWII theatre with all units plus command structure, with thousands of players playing on the same server, but most people never even heard of that game, let alone play it - Battlefield 1942 was "mainstream" version of a sort, and it got its recognition.

EDIT: I completely missed that Combat Mission: Barbarossa to Berlin (tactical war strategy) is from that year, which automatically makes it my favourite game from that year, given that I still play it to this day. BF1942 still as my vote for GotY.

Some more greats arrived this year with

Ratchet and Clank was an instant hit for us, never missed a single release since

Such a fun shooter platformer with the most satisfying bolt collecting sound ever.

Need for Speed Hot Pursuit 2 was a personal favorite. Police chases are always fun

Back when the franchise was still great.

Sly Cooper also started in 2002, games I didn't play until the collection came out on ps3 where I played them back 2 back

Start of a great series with tons of charm and clever gameplay. Psychonauts likely drew a lot of inspiration from Sly.
Underrated game series, it deserves a comeback just like R&C and Psychonauts.

This is the year Ikaruga came out on GameCube, awesome game yet initially released in 2001


Eternal Darkness was something else, testing the player's mind as much as their abilities.

I would love to play a modern remake of this.

Plenty great sequels this year as well with RCT2 leading the pack for me, yet the best game of 2002 for me is Windwaker

It's the perfect Zelda game for me. Perfect balance between open world, dungeons and story. And being able to turn the wind in the right direction is genius in a game where you sail around a lot. Sailing around was perfection as well, so relaxing, so great to find new islands to explore. 10/10.

For me it is Mafia: The City of Lost Heaven on PC, I played it religiously many times.

Metroid wins this handily for me, despite my beloved Wind Waker being in the mix. Metroid Prime is in my top 10 favorite games of all time. The only other games that rank that high for me this entire decade are Majora's Mask and Bioshock... and I like Prime better than both.

WInd Waker was great (if a bit unfinished feeling), REmake was fantastic and I loved Eternal Darkness. Oh, and Splinter Cell was incredible; showed Metal Gear how it's done on the first try.

Metroid Prime is such a masterful jump to 3D. It’s crazy how unique these games still are, I can’t really think of any other metroidvanias in 3D, other than maybe the first Dark Souls?

This is a difficult year that saddens me a lot. The game I played the most from games released this year is by far Warcraft 3. The campaign is awesome but the mods and community created content is what elevated this game to legendary status. So many spin off genres started or got popularized in the Warcraft 3 motor. But then Blizzard in a spiteful mode for loosing the Dota name effectively killed the mods in the update released with the train-wreck Warcraft 3 reforged. Any mods would automatically be Blizzard owned going forward. Old maps and mods disappeared. It is still possible to play on private servers using one of the older patches of the game I've heard, something I have yet to try out.
If it was not for the fact that I try to judge games based on my enjoyment of playing them today in their current state Warcraft 3 would be a top 10 game ever for me.

The Gamecube had probably its best year. The legend of Zelda the Wind Waker got scuffed at for its art direction but visiting it today the world is still a marvel of beauty and have aged considerable better visually then the brother Twilight Princess. Metroid Prime surprised the gamers and Nintendo alike bringing the Metroid franchise in to the 3D realm with affirmation and is one of the best looking games of the generation. Resident evil started to make the Gamecube its home pawing the way for my favorite game ever a few years down the line. Another survival horror game saw the light (or darkness) the same year. Eternal Darkness is still unmatched when it comes to third wall braking in games. Mario Sunshine my least favorite of the 3d Marios but not without its fans also released in 2002.

The first Kingdom Hearts made Donald and Goofy action heroes. A blend of multiple genres and spawning several loved Disney worlds it is my favorite in the series. Many consider the second game superior, but I felt that the streamlined direction and awful first few hours of the second game lost my interest. Exploring the settings with double jumps and gliding in the air was more fun for me even if it lacked a lot of polish.

My vote goes to other this time around. A fantastic game got released in Japan for the GBA. A series that had yet to see a western release. Only really played it recently with fan translations since it has not got an official release outside of Japan. I struggle to choose between my favorite game in the series between it and the first western release of Fire Emblem. But no matter which of them I like more, Fire Emblem: Fūin no Tsurugi, aka Fire Emblem the Binding Blade is my game of the year.