[quote name='antlp89']Bioshock.[/QUOTE]
Seconded.
Some other good ones were Hotel Dusk, MGS3, Half-Life 2, Braid, Shadow of the Colossus, Heavy Rain, and Indigo Prophecy (for the most part).
And I really like Left 4 Dead's minimal story decision, so I'll throw that in here since everyone mentioned it in the "worst plots" thread.