I can't decide on my favorite. There's always a part of me that wants to go with Minecraft simply because of the ridiculous amount of mods, maps, and plugins. The base game itself is really boring IMO and each update seems to add just a few random, mediocre features and set all the good modders back a month. But the things people have done with it, with adventure maps, redstone wiring, server plugins, and mods, make the game almost infinitely versatile.
But that's just from a pure gameplay perspective, and I've always been the kind of person to appreciate a compelling story in my games. And that award goes uncontested to Nine Hours, Nine Persons, Nine Doors. The puzzles, tiresome as they were to have to go through multiple times, were all solid, challenging, but understandable, and were all structured in a way so you could complete them much faster on subsequent playthroughs, unlike many other point-and-click games. The story is masterfully written and is paced so the player never sees a twist or death happening (though on repeat plays you can pick up on the foreshadowing). It's a very atmospheric story; the player is always kept in some level of suspense until the very end, and when the game does hit you, it hits hard. There are six endings to the game, two of which are the True Ending and the Safe Ending (which must be completed before the True Ending can be achieved; there is a reason for this, and like the rest of the story it is amazing), and those two endings both made me feel in ways that still haunt me in subsequent playthroughs. Some stories can bring tears to your eyes, but when I first finished the Safe ending I felt the wind knocked out of me and I held my DS in a state of zombielike bewilderment until enough sense finally returned to me so that I could shed a bathtub of manly tears.
I'm not sure if 999 is the best game I've played, but it is the best story I've experienced. The recent sequel, Virtue's Last Reward, was also great and by the end of the game made sense (a rarity for mystery-based stories), but I felt it wasn't held together as well as the first game: I found myself caring for the characters less, and the sci-fi atmosphere didn't play with my emotions as much as the horror atmosphere of the first game did (and more of that would have been ideal for a theme centered on betrayal). But it was still plenty worthwhile, and each of the 9 "real" endings held something meaningful to them. Looking forward to the third game.
Of course, if Starbound's half as good as it seems then the entire rest of the post is practically moot.