I would say Half Life 2, but I haven't finished playing it yet. (Though the fact I was able to play the game after being spoiled by FF13 graphics says something about it. Had to take a break from Ravenhold though, that shit is creepy.)
Games I have finished:
Mass Effect 1. I liked 2 better, but the first one had a better storyline, while the second had better, well, everything else.
Kotor 1 had an awesome story for its time, I think.
Bioshock 1, though I heard it's so much like system shock that it really can't count as an original storyline...
Surprisingly, Lunar Silver Star Harmony or whatever it's called.
The Halo series as a whole, though standalone Halo 1 had the best storyline.
And The Force Unleashed. They did a surprising job fitting the storyline together.
I think that's it, probably forgot some but there you go.