I love the Kingdom Hearts series as a whole, but my favorite has to be Birth By Sleep. Out of all the games, the pacing is the best, the storyline just works with integrating the Disney worlds the best, the battle systems/gameplay is the best, and my three favorite characters in the series are in this game.
Also, I enjoy the Ace Attorney series, Pokemon (main series and Mystery Dungeon), Final Fantasy, Animal Crossing, Dangan Ronpa, Legend of Zelda, and the Legend of Spyro trilogy. Also kind of like Skylanders, 'cause collecting shit is fun.
Don't think it counts as a "game" since it is strictly a visual novel and not playable at all, but I also like the When They Cry series, Umineko being my favorite.
Suikoden II - some of best memories of my childhood with this lovely RPG on the PSX
Some of the runner's up would be (although could still probably add another 50 games easily stopped at PS2 haha)
Shadow Hearts series/FFX - PS2
Dino Crisis2/FFIX/Tombi - PSX
Dragon quest series / Dragon warrior monster series - GB/GBA
Banjo Kazooie/Mystical Ninja Goemon/LoZ - OOT/Smash Bros - N64
Alex Kidd/original Sonic/Wonder Boy series - SMS