This is a discussion on what you think are games with some of the greatest stories you've ever experienced in a video game. Please don't just list games, explain what about them made your list. Here are a few of mine.
Final Fantasy X (PS2)
What makes this story great is how it builds on the character relationships before several plot twists come around and you realize that some of the main characters you've been playing with for hours are not going to have a happy ending.
Metal Gear Solid 2 (PS2)
Say what you want about the character switch and convulted ending (I partially agree) the scene about Emma and the bird is one of the saddest moments in gaming. Cheers to superb voice-acting.
Xenosaga Trilogy (PS2)
While the 3rd game had to wrap the series up faster than intended, the story in these games was enough to get me to play through all 3 in a matter of months. Again, great voice acting and plot build up.
Skies of Arcadia: Legends (GCN)
It really could have used voice-acting, but the music helped set the mood in this tale of an empire trying to take away the free skies from mostly-good air pirates.

Final Fantasy X is the best video game storyline I've ever personally experienced, but I also have to give a nod to Terranigma and Zelda: Link's Awakening, both of which are also very moving and surprising in places.

@Corbie-I've yet to experience Terranigma but I've heard a lot of good about it.

Kingdom Hearts series The story in this series is pretty good but I'm adding it to the list because I think it does the "musical opening/closing" narrative better than just about any game. Feel free to disagree!

I'd have to go for Bioshock as one of the best. It wasn't just the story, but the way it was woven into the game in such a cinematic way.
As for Metal Gear Solid 2, though, I think Objection Blaster might be in the minority there. I mean, there was a lot to enjoy about the story, but by the end it just got buried in so much nonsense that it fell apart.

The World Ends With You or Warcraft III.
BioShock wasn't that great, and did Link's Awakening even have a story?

Majora's Mask, for me. And if we include PC games, Freddy Pharkas: Frontier Pharmacist. (No, really!)

@The Fox-Actually, I said I partially agree with such complaints. The ending WAS pretty "wtf?". I think part of it might have something to do with 9/11 leading to them changing parts of the ending...or Kojima is just weird,

The game Full Throttle on PC because it's about bikers in a futuristic world and it has some unbelievably clever strategy parts in the game that just blow your mind. Think Monkey Island, but with bikers and a plot about murder and detective work.

Another great game that doesn't get the kudos it deserves is X-Wing for the PC. This was an old game from the early 90's (I was 7 when I completed it) and the flights were amazing. The controls were smooth and there wasn't much to the story other than reading about the story and missions in the War Room. The entire story could be re-read when you finish every mission, making the story a smooth read through.

I would Have to say:Jak&Daxter series story was very well thought out & Fable 1 storyline was also very compelling what happend to Maze in the game was a shocker to me.So those are my favorite video game stories,I do have some other good ones but you only asked for our favorites.

Valkyria Chronicles has a great storyline involving many interesting twists and lots of depth in every character. Even all the seperate troops you assign to your squad have backstories and developing stories as the game goes on, although they're only updated in text, as opposed to cutscenes like the main players of the game. In all, it's a very light-hearted kind of game, whith many different themes going for it and lots to keep you interested aside from gameplay. Many sad moments and some you may ot may not find sad depending on whether or not you have a soul.

As you can tell, I love this game.

Muscle March

@Chicken Brutus:Muscle March,ROFL,well it looks as if you might be correct there Chicken Brutus.lol

Baiten Kaitos: eternal wings and lost oceans

The plot twists will make you crap your pants

I second Link's Awakening and raise you a Final Fantasy VI! (note: not 7, **** 7)

@Malnin-I got about 10 to 15 hrs into that game...then I succumbed to the awful voices/music and annoying dungeons. WIsh I could force myself to get far enough that interesting things happened int he sotry (I recently tried to) but I always fail to do so. Just my opinion.

@Kim Jong-Il: The World Ends with You is probably the most original thing Square has had a hand in in years. Definitely agreeing with you there.

Also, Suikoden II has been my favorite game ever since I played it for the first time. It follows the story of two boys who each gain a half of one of the 27 True Runes and, thanks to its power, end up each working to stop the war occurring in the game, but in radically (tragically?) different ways. If ever there was a game where you want to get the 'best' ending, this is it, IMO. It's a long game if you're looking to complete it fully (longer if you take time to play through the first game to its 'best' ending so that you can recruit the main Suikoden character and his servant, who gives you like the best recipe for the cooking battles in the game, but i ramble) and if you take time to keep your characters leveled (a must for the Luca Blight three-part battle, to be honest). (almost) every single recruitable character has an interesting backstory that adds to the richness of the plot (especially if you play the games in order, but it's not absolutely necessary to understand the plot), and the sidequests are really fun(ny), too.

It is not worth the $120+ people want for it on eBay, though.

I thought Mass Effect was well done as well, but that might just be because I'm a sucker for Bioware.

I third the TWEWY nominations. That was some of the best story presentation on DS yet. That whole game was awesome, except the combat which was only above average for me. However the story and style of the game from the music to the art style really drew me in. I need to play through it again, I beat it way back in October...I just found out when I booted it and got 262 days of badge points...

@Objection_Blaster: TWEWY's combat didn't really do it for me either (it was interesting, but i could never really get the hang of the top-screen combo stuff). I loved how it had instant replay value in the form of the secret reports, though (even more plot awesomeness to discover; not many games are like that), and that you can muck around with the levels of your enemies in order to breeze through the story or get different items from them to sell/for quest requirements.

Majora's Mask and Eternal Darkness