1. Dark Souls- Easily my favorite. I haven't finished Skyrim yet but I don't see this changing. Demons Souls was my game of 09 and this is a more complete realization of what that game was.
2. Deus Ex. Even with the shitty boss fights and meh ending, I loved this game. I enjoyed the story, the setting, the atmosphere. I hope the do at least one more game leading up to the time of the original.
3. Xenoblade Chronicles. I'm halfway tempted to wait until this year for the US release, but I've played too much of it to ignore it and it wouldn't have the same impact then anyway. Its just a good JRPG that expands a bit on FFXII's combat and grand scale.
4. Radiant Historia. I've never spent 50 hrs on a portable game before.
5. Legend of Heroes: Trails in the Sky. and have done it only one other time since
6. Skyrim: When all is said and done, it may climb higher, I've got about 35 hours in so far. I'm one of the few that really liked exploring vanilla Oblivion and this is better in every way.
7. Portal 2. Just recently finished this. The game is honestly pretty dull until the first main twist and getting to explore beyond the testing grounds and Cave Johnson make it a lot more interesting. I felt satisfied at the end.
8. Batman: Arkham City. Definitely one of the best of the year but just not as good as the original. All in all the game may be longer than AA, but the main story is surprisingly short and I haven't felt any of theside missions as compelling. I may enjoy it more when I don't feel like I have to finish it in a hurry.
9. NBA 2K12: The my player role playing is addictive. I'd like to see them expand on it a bit.
10. Two Worlds 2: And here's the oddball. My problem here is I have a lot of GOTY contenders like Skyward Sword, Saints Row the 3rd, Gears of War 3 other games like Bulletstorm, MK, etc. Problem is I haven't played any of them. Two Worlds came out here in the US almost exactly a year ago and despite the jank, I really enjoyed the game. Its unfortunate that the games climax comes out of nowhere, certain plot points are completely dropped, and the largest area of the game you never really get to explore at all. Despite that I found it one of the better gaming experiences this year. To be honest I'd almost put Fishing Resort here. That game is pretty fun.
Honorable Mention: Fishing Resort. If you have a Wii and like easy going exploring type games, Fishing Resort is for you. Really well made, great for all ages and genders.
Honorable Mention 2: I think the OP said I get two honorable mentions. Venetica gets my second HM for all the reasons TWII did. It came out when I had nothing else to play, really low expectations and surprisingly fun despite all the jank.