1. Mass Effect series
Sure the 2nd one is my fave but can't count one, without including the other. The Mass Effect franchise certainly has one of the best stories in a sci-fi game, set in space but that's not the reason why I love it so much. It's the believable galactic setting and I just like how Bioware slowly but continuously feeds the player with information on the different worlds, systems, races and technologies. I'm just fascinated by the possibilities of future technology and space travel and it's the same reason why I like novels such as "The Foundation saga" by Isaac Asimov.
The characters are also a major reason and it's great being able to get to know all of them, whilst getting accustomed to the traits and mannerism of each race. So to Bioware... thank you and I'm expecting great things from Mass Effect 3. ^_^
2. Fallout 3
I've played this game for God knows how many hours and I've still yet to complete my 1st playthrough. It's just one of those game where you can spend hours just roaming around the environment, completely immersed in doing whatever you wanna do. Playing this game is like living a 2nd life... with an overarching story/quest behind it.
3. Rome Total War
Probably my favorite RTS game of all-time and the singleplayer is the main reason why, since it has the most replay value of any game I've played. I just like completing the campaign as one of the Roman factions, only to play again as an Arab faction and then again as a Mediterranean faction, yet again as another Roman faction and they each play fairly differently. See what I mean... replay value.