Fun article. I just can't believe that Star Ware: Knights of the Old Republic didn't make it in there. That was the biggest for me. Probably even more so than Bioshock.
How about Assassin's Creed? After killing Robert de Sable, *spoilers* you realize that your master tried to get that super powered orb all for himself. And you just killed everyone who tried to take it from him. And then he WOULD rule over everything, of course, were it not for you. And then the whole plot kicking in then credits thing... But you knew those scientists were Templars a little earlier... *end spoilers*
Yes, Fighters guild was the quest line. To this day I still play oblivion like I just picked it up. Bioshock was one of my favourite storys ever. It is really the only horror game I play. Also loved SotC, I remember picking it up with my friend, thinking, this looks neat... not knowing the power it was about to unleash on us lol.
Ahh, Deus Ex. Even if I disliked the endings, the game really allowed you to choose the way you could deal with your goals and convictions in a unique fashion. Loved it.
Jade Empire has a good twist, where your kind and gentle kung-fu master turns out to have been manipulating you as part of his grand plan to overthrow the Emperor (his brother) and install himself as evil leader.
I don't know about the rest of you, but when Me and my brother were playing Bioshock and we got to the twist, we just couldn't believe it. We had always thought Ryan was the bad guy, but turns out YOU'RE the bad guy. UNbelievable, but a masterpiece of storytelling.
I remember FFIV on the original snes. Due to the twist at the start, I'm starting to find most modern game plots lame. Latest good game plots are battlefield bad company, cus its actually funny, and gears of war 2 purely because it is so well done.
Also I must mention something about Braid. I've heard on many a site that the plot also does not involve a princess, but she is like a term to describe a nuclear bomb, and Tim is a bomb scientist who has ruined the life and distorted time with his bomb.