.hack gets my award for originality, but I wouldn't call it my favourite story.
Half Life's story angered me because it made no sense when I played through the game. Then when I read all the official sources and stuff about what actually went on it sort of felt cheap and like Valve made it all up AFTER half life was released. Sort of like:
"Well, we're done! We released Half-Life!...OH [img]/xxx.gif[/img][img]/xxx.gif[/img][img]/xxx.gif[/img][img]/xxx.gif[/img] WE FORGOT A STORYLINE."
Anyways, Syberia still holds the title for best storyline in my eyes. It managed to be personal yet epic in scope, and had many emotional twists and advancements. The sub-plot that was unraveled over Kate's cellphone was very dramatic too, and is almost on par with the game's main story (and could've been better than it too, but it was all done over cellphones, so it wasn't quite as awe-inspiring).
(SPOILER)When Kate finally abandons her job, home, and fiance to go after Syberia, it's all very dramatic and emotionalI love it.