The 2012 Game of the Year is Journey.
The runner up is Dragon's Dogma.
The master thread for all of these contests can be found here.

This year definitely needs a runoff vote.  We ended up with 38.6% "Other" votes which is the most we've ever had by far.  Only 3 games made the cut to the runoff round, and they are joined by 4 write-in candidates.  First the games that made the cut:

Diablo III (PC/Mac)
It’s time to face the devil again.  The third installment in this diabolical franchise would sell over 12 million copies across all platforms.

Journey (PS3)
Don’t Stop Believing in this indie PS3 game.  The unique multiplayer system allows you to Journey with the other players you meet or go your Separate Ways.  Any Way You Want It.  This game scored a 92 on Metacritic and has sold over 6 million copies.

Fire Emblem: Awakening (3DS)
The annual, amazing Nintendo game ended up coming from the Fire Emblem franchise in 2012.  This ensured that Smash Bros would get many Fire Emblem characters in the years to come.  Fire Emblem: Awakening scored a 92 on Metacritic and sold over 2.3 million copies.

Here are the 4 new games that each got more than one write-in vote:

Dragon's Dogma (PS3/XBox360)
Since 2011 had both Dark Souls and Skyrim, it was natural for many people to look for another 3D fantasy RPG in 2012.  The best of these was arguably Dragon's Dogma, Capcom's first attempt at an open-world fantasy game.  Since 2012, the game has been released on several other platforms and has sold over 7 million copies.  There is also currently a trailer out for a very impressive looking sequel that is on the way.

Spec Ops: The Line (PS3/XBox360/PC)
This tenth entry in the Spec Ops series was also a reboot.

The Walking Dead: Season One (PS3/XBox360/PC)
Telltale Games had gotten a reputation for making Adventure games that removed the puzzle requirements.  The most beloved of these was arguably The Walking Dead series, based on a comic book by the same name.  The Walking Dead was released in episodes starting in 2012.  Currently over 28 million episodes have been sold for Season One.

ZombieU (Wii U)
This seems to be the year for zombie games.  ZombiU arguably made better use of the Wii U gamepad than any other Wii U launch title.  ZombiU was the best selling third-party launch title for the Wii U, but it was still unprofitable for Ubisoft.

Runoff voting for 2012 Game of the Year will end on Sunday, Dec 3 at 11:59 PM, EST.

Games that didn't make the cut:

Halo 4 (XBox 360)
Borderlands 2 (PS3/XBox 360/PC/Mac)
Dishonored (PS3/XBox 360/PC)
Far Cry 3 (PS3/XBox 360/PC)
Mass Effect 3 (PS3/XBox 360/PC)
XCOM: Enemy Unknown (PS3/XBox 360/PC)

Here are some other notable games for 2012:

Blazblue: Chrono Phantasma (Arcade)
Candy Crush Saga (Mobile)
Chaos Rings II (Mobile)
Clash of Clans (Mobile)
Puzzle and Dragons (Mobile)
Guildwars 2 (PC)
Hotline Miami (PC)
Legend of Grimrock (PC/Linux)
Slender: The Eight Pages (PC/Mac)
Thirty Flights of Loving (PC/Mac/Linux)
Torchlight II (PC)
Pokémon Black2/White2 (DS)
Danganronpa 2: Goodbye Despair (PSP)
Dust: An Elysian Tale (XBox 360)
Fez (XBox 360)
Mark of the Ninja (XBox 360/PC)
Trials Evolution (XBox 360)
Assassin’s Creed III (PS3/XBox 360/Wii U/PC)
Call of Duty: Black Ops II (PS3/XBox 360/Wii U/PC)
Dragon’s Dogma (PS3/XBox 360)
Max Payne 3 (PS3/XBox 360/PC)
Need for Speed: Most Wanted (PS3/XBox 360/PC/Vita/Mobile)
Persona 4: Arena (Arcade/PS3/XBox 360)
The Walking Dead (PS3/XBox 360/PC/Mobile)
Yakuza 5 (PS3)
Animal Crossing: New Leaf (3DS)
Bravely Default (3DS)
Fantasy Life (3DS)
Kid Icarus Uprising (3DS)
Kingdom Hearts 3D Dream Drop Distance (3DS)
New Super Mario Bros 2 (3DS)
Paper Mario: Sticker Star (3DS)
Super Stardust Delta (Vita)
Zero Escape: Virtue's Last Reward (Vita)
New Super Mario Bros U (Wii U)
Nintendoland (Wii U)

Dishonored! I've never been much of a stealth fan but Dishonored changed that and got me hooked on Arkane. I loved the setting, story, and combat/abilities. I will give an honorable shoutout to Dragon's Dogma! 

Diablo 3 was one of the biggest letdowns in gaming history and marked the beginning of the end for the Blizzard I once loved.

Zombi U was my favorite game that year. It was frightening to play. My adrenaline couldn’t take another play through. Plus sniping with the game pad was awesome fun!

I'll have to think about this some more, but some omissions I think others might find worthy include Counter-Strike: Global Offensive, Crusader Kings II, and Euro Truck Simulator 2.

Black Ops II

I know it's cool to bash COD, but this one was a genuinely excellent shooter, with a strong campaign bolstered by branching story paths and tons of variety. Plus, as a Wii U launch title, we could finally play with pointer controls without having to sacrifice graphics, which was awesome.

Pretty shocked The Walking Dead didn't make the poll. Haven't played it myself, but it was considered GotY by many at the time.

Anyways my choice is the controversial Diablo III, best gameplay in a topdown ARPG hands down.

Honestly a quite solid year in my book, four titles I really loved: Diablo 3, Xillia 2, Virtue's Last Reward and Borderlands 2. To be fair D3 would admittedly be at the bottom of those four if we're comparing the games at launch, but it would still be in the top 4. Rounding out my top 5 would be Mass Effect 3, another controversial 3 that was better than people gave it credit for.

1. Diablo III
2. Tales of Xillia 2
3. Zero Escape: Virtue's Last Reward
4. Borderlands 2
5. Mass Effect 3

2012 was a banger year, well going by Japanese release dates for Fire Emblem and Animal Crossing.
Fire Emblem: Awakening, The Walking Dead: Season One, and Animal Crossing: New Leaf are all amazing games.
I'll give the vote to Fire Emblem: Awakening.

During 2012 I got more and more into the 3DS as the Wii and PS3 were winding down. My Guitar Hero addiction had waned as well by this time but I continued what I started last year; re-buying stuff from my family's past and hunting down games I missed but wanted to play. At the end of the year I did also get the WiiU.

From the list I played Diablo 3 and Fire Emblem Awakening, but Diablo not until it released on Switch and I never completed Fire Emblem. From the 'other' list I played Kid Icarus Uprising, New Super Mario Bros 2, New Super Mario Bros U and Nintendoland. Those last two I got with the system on release. The 3DS games were both fine, but they wouldn't become a favourite.

Besides those I played Professor Layton and the Miracle Mask, ZombiU and a little game called Resident Evil Revelations. Professor Layton was like any in the series, which was good, but I had gotten a little disinterested and never completed it. Resident Evil Revelations though was excellent. I couldn't believe such a game could be on 3DS. It was exciting, looked great, had a fun story with good bosses and levels and some decent side modes. This would become my favourite 3DS game, on a system that actually hosts a lot of great games.

My vote for this year easily goes to other, for Resident Evil Revelations. Should've been at least mentioned in the OP posts if you asked me.

I have a feeling I'm forgetting some game from this year, but I'm going for Journey here. Other highlights from 2012 would be Dishonored, Borderlands 2 (in co-op), Dust: An Elysian Tale, Fez, and Legend of Grimrock.