Several great games this year, but the game that is in my opinion the best of 2006 isn't even listed, so I'll have to vote other this time.
Okami remains one of the best games of its kind, outdoing most Zelda games in their own game. The visual style is timeless and absolutely corgeous, and the celestial brush was a stroke of genius, turning the gameplay into a wonderful puzzle and the world into an interactive, living thing.
Final Fantasy XII made an obvious effort to detach itself from the series' past, and for the most part it was a success. It has been a long time since I last played it, and I've heard the Zodiac Age rerelease has even improved the game in a lot of areas, so it's possible in the future my opinion on it could even improve, but as of now it remains beneath the best games in the franchise.
Ultimately, the choice here was easy. The Legend of Heroes: Trails in the Sky SC was first released in Japan in 2006, and since it's the only game from this year in my top 10 of all time that makes my pick obvious. It's unlikely to win since very few people have actually played these games, but it still gets my vote. Some of my all-time favourite characters, a great, vast story spanning over ten different games, excellent battle system, and a great soundtrack all make this one of the best games ever.