I wouldn't be able to narrow it down to an individual storyline that I thought was better than all others. But the Silent Hill series is easily one of my all time favorites. In fact, I think that the entirety of SH 1-3 were all quite fantastic. But, as I said, I wouldn't be able to choose one game or series that I thought was far superior enough to justify them being my favorite. Not saying that none of them are good, by any stretch of the imagination, but some of my favorites are as follows:harhol said:Objectively: Silent Hill 2
SH Series- You already knew this, I chose this simply because the story really is fantastic. It focuses a lot on the protagonist as they fail in few endeavors, and succeed in even less. However, the story line still makes adequate room for its supporting characters to be further developed. Most of the time, it's pretty damn unsettling, and more often than not, downright scary. Interestingly enough, some of the character progression helps to push this along. Also, it's one of my favorite series anyway, so really, I couldn't not mention it.
Call of Cthulhu
There are, of course more, knowing me, I've probably got some lengthy patch of text to accompany it, but I really can't think of anything else at time of writing.