1. Starcraft 1, 2 (As an e-sport and as a life pursuit)
2. Fallouts 3 and NV (In terms of immersion and immensiveness. Only DLC like Point Lookout and Sierra Madre come close to a neat perfection. Gameplay, btw, is a weak point of the series.)
3. Mass Effect 2 (Best storytelling yet in an RPG. There's still room for improvement, though)
Very Honorable Mention to
4. Portal (for its stimulating gameplay and black comedy)
5. Silent Hill 1,2 as well as Dead Space 1, 2 (Horror really reaches another level in video game format. Still left wanting something more, though.)
Note, a shooter would be needed in a desert island scenario, but good luck naming one as an innovative flagship of the genre.