The 2009 Game of the Year is Uncharted 2: Among Thieves.
The runner up is Batman: Arkham Asylum.
The master thread for all of these contests can be found here.

There was a tie, and there needs to be a second round of runoff voting.  This time it's down to two games:

Batman: Arkham Asylum (PS3/XBox 360/PC)
This first “Batman Arkham” game impressed critics to the point that it received the Guiness World Record for “Most Critically Acclaimed Superhero Game Ever”.  They weren’t joking around when they gave Batman: Arkham Asylum 91-92 review scores on Metacritic.  The game has also sold over 4.3 million copies worldwide.

Uncharted 2: Among Thieves (PS3)
This second entry put Uncharted on the map.  It received an impressive 96 on Metacritic and sold over 6 million copies.

Runoff voting, second round, for 2009 Game of the Year will end on Monday, Nov 20 at 11:59 PM, EST.

Games that didn't make the first cut to the runoff round:

League of Legends (PC)
Assassin’s Creed 2 (PS3/XBox 360)
Bayonetta (PS3/XBox 360)
Call of Duty: Modern Warfare 2 (PS3/XBox 360/PC)
New Super Mario Bros Wii (Wii)
Wii Sports Resort (Wii)

Games that didn't make the second cut:

Demon’s Souls (PS3)
Left for Dead 2 (PC/XBox 360)
Ratchet and Clank Future: A Crack in Time (PS3) 

A quick reminder that you cannot vote for Pokémon HeartGold/SoulSilver this year.  The time to do that would have been 1999 with the original Pokémon Gold/Silver. 

However, here are some other notable games released in 2009 that you can vote for:

Blazblue: Continuum Shift (Arcade)
Angry Birds (Mobile)
Plants vs Zombies (PC/Mac)
The Sims 3 (PC/Mac/Mobile)
Gran Turismo (PSP)
Half-Minute Hero (PSP)
Dragon Quest IX (DS)
GTA: Chinatown Wars (DS/PSP)
Mario and Luigi: Bowser’s Inside Story (DS)
Might and Magic: Clash of Heroes (DS)
LoZ: Spirit Tracks (DS)
Forza Motorsport 3 (XBox 360)
Halo 3: ODST (XBox 360)
Halo Wars (XBox 360)
Left for Dead 2 (XBox 360)
Shadow Complex (XBox 360)
Trials HD (XBox 360)
The Beatles: Rock Band (PS3/XBox 360/Wii)
Borderlands (PS3/XBox 360/PC)
Dragon Age: Origins (PS3/XBox 360/PC/Mac)
DJ Hero (PS3/XBox 360/Wii/PS2)
Guitar Hero 5 (PS3/XBox 360/Wii/PS2)
Need For Speed: Shift (PS3/XBox 360/PC/PSP/Mobile)
Resident Evil 5 (PS3/XBox 360/PC)
Final Fantasy XIII (PS3)
Infamous (PS3)
Killzone 2 (PS3)
Pixeljunk Shooter (PS3)
Ratchet and Clank Future: A Crack in Time (PS3)
Trine (PS3/PC)
Boom Blox Bash Party (Wii)
Just Dance (Wii)
Little King’s Story (Wii)
Mario and Sonic at the Olympic Winter Games (Wii/DS)
Monster Hunter Tri (Wii)
Punch-Out!! (Wii)
Wii Fit Plus (Wii)

Punch-Out!! for me. Good year though.

it has to be Demon's Souls for me. I love how back then, Souls-like wasn't a "genre", Demon's Souls was just an exceptional action RPG with a lot of clever twists

Demon’s Souls, for me. A brilliant action-RPG with exceptional art direction, impressive environmental storytelling, riveting risk-versus-reward combat, and an amazing sense of discovery — not just in terms of physical locations and treasures, but game mechanics.

Demon, given it is still amazing to this day. The remake is superb. And it basically started its own genre.

Uncharted 2 for me. But I do have much love for DemonS and Bayonetta. I also have a soft spot for Batman AA.
Having all that said, kinda slow year tho.

Arkham Asylum and Dirt2

Uncharted 2 for me. The best of the series, loved the set pieces (Nepal, Shambala), the gameplay is better refined than the first and doesn't include forced first fights like the third. The story is a fun "Indiana Jones" type adventure and Chloe is a great addition to the cast.

Bayonetta is the only real answer. Anything else is wrong.