An extremely polished and beautiful underwater adventure game in the tradition of Metroid and Castlevania. Explore dark caves, colorful coral reefs, sunlit oases, and more as you play Naija, a lone water dweller in search of her family. The mouse–driven controls are wonderfully intuitive, the world is massive and teaming with secrets, the graphics and sound are gorgeous... it's little wonder that this game won the Grand Prize at the Independent Games Festival, and was rated 9/10 by Wired Magazine.
One of the best platformers ever released for the PC. In Gish, you play a 12-pound ball of tar in search of true love. Become slippery to slide through small places, sticky to climb up walls and ceilings, and rock hard to force your way through barriers. The game's physics engine, along with all of its production values make this one a real pleasure to play.
Be forewarned: this game takes time and dedication to appreciate. However, if you take that time, you will find in Dwarf Fortress one of the most amazing and complex simulation games that you will ever play. Combining aspects of roguelike, strategy, and "god" games, Dwarf Fortress has two modes of play: Fortress, where you oversee a dwarven civilization, and Adventure Mode, which plays like a typical roguelike game. To date I find Dwarf Fortress to be one of the most amazing games ever made, including all commercial offerings, but like I said: be warned that the game is not easily accessible! For help, look to the wiki. Also, try out Mike Mayday's Graphics Edition of the game.
Among the best independent games released in the last ten years, Cave Story is a traditional action adventure in the vein of old classics such as Metroid and Castlevania. It was five years in the making, and every detail shows off the love and care that went into its production. If you only play one indie game this year, make it this one.