Top THREE? Only three? Ugh.
Allright.... though this list shifts a bit from time to time, but the top 10-15 remain in their group even if they randomly shift positions based on my memory & mood at the time.
#1: Minecraft (PC). This doesnt leave it's top position. Easily my favorite and I've put countless hours into it. No matter how much I play it, there's always more to do. More to build, more to dig, more monsters to fight, more adventures to be had.... particularly when mods are involved (at which point the amount of content available can get a little silly, particularly with the big modpacks), but I play vanilla too.
#2: Baroque (PS2, Wii). An action roguelike, in 3D (not 2D like many are), with a third-person view. A huge game with lots of content, and a very mean learning curve. An absolutely spectacular game, and one that I've put a few hundred hours into.... yet even I have not completed 100% of everything. Has a wonderful dark, freaky aesthetic to the graphics/art, and creative and messed up monster designs.
#3: Dodonpachi Daifukkatsu (360, JP import). I love shmups, particularly danmaku types, and Cave makes the best of them as far as I'm concerned. To me, this game is the best out of the ones they've made, particularly the 360 versions. There are two versions of these, normal and Black Label, and when put together they add up to ALOT of different modes and such. A brilliant game to start with, all these additional modes just make it even better.