1. Nier

2. Yakuza 3

3. Bioshock/The Darkness

Seriously, where did you find a keyboard with an "origami button"?

1. The World Ends With You

2. Bioshock

3. Final Fantasy XIII

I can't make a list without writing the reasons why I choose what I choose.  So here I go again:

1.  Heavy Rain: I'm not sure people appreciate what this game has done.  Yes, it has some plot holes but look at how it handled the mature themes that other games (ie: Mass Effect) got crucified for.  There was crimes against children, sexual situations, attempted rape--things that had no business being in a video game but Heavy Rain handled them maturely and masterfully.  At the same time, it offered up plot twists and characterization in a way that most series could only dream of.  There were moments that had me on the edge of my seat and moments that felt more intense than any fighting game or fps on the market.  I was compelled to play "just one more hour" because of how engrossed I was in the story. That's the highest praise I can give this game--aside from Madison's sexy booty.  Dat ass.  Dat ass, indeed.

2.  Enslaved: Odyssey to the West:  In an apocalyptic future, a young woman forces a man to keep her alive while she makes her way home.  A simple story but the way the story is told, the way these characters feel like real people, and the bigger picture of things at work, left quite an impression on me.  You're not going to play this game anyway so here's a spoiler:  The part where Trip finally sets Monkey free from his slave headband and he asks, "What the hell are you doing?  Put it back on.", gave me chills.  It's hard to find new stories to tell so, a lot of the time, it's the way a story is told that makes it great.  The transformation of both of these characters into what they were in the end of this game are what made it great.  I hope we get a sequel.

3.  Lost Odyssey:  JRPG's are often about a group of unlikely heroes forced to band together to save the universe.  Lost Odyssey was no different.  What made the story great was the interactions between the characters--some of them, immortal.  The "memories" short stories did the impossible:  made me look forward to reading in a video game.  There were a couple of moments where I just smiled to myself and thought, "This is just perfect".  This game's story made me laugh, almost made me cry (If I weren't so manly, I probably would have....), and always had me engrossed.  There were a couple of cringe worthy moments but on the whole, Lost Odyssey's story was the main event over its great graphics, music, battle system, and scope--and that's saying a lot.

--I haven't completed:  Bioshock, Red Dead Redemption, or Assassins Creed 2 (which is why I haven't bought Brotherhood, yet), or Valkyria Chronicles.  These games feature great stories, as well.  Mass Effect (series) story isn't quite complete yet since it's a trilogy.  Uncharted 1 & 2 featured tight storytelling but was a little too predictable. 

Totally agree - my faviourite game of 2010.

1. Tactics Ogre: Let Us Cling Together (okay its a remake, but no game story is as well written this gen!)

2. Assassin's Creed 1 (story from 2 wasnt as good imo).

3. Castlevania: Lords of Shadow - story isnt that original, but the presetation and delivery is excellent and what an ending.

1- Kingdom hearts : Birth by sleep

2- MGS4 : Guns of the Patriots

3- God of War III

1- Professor layton and the curious village

2- TWEWY

3- Ace attorney

that's cheating haha :P. Otherwise a lot more people would put chrono trigger (I wouldn't, I'd put TO but heh)

Plus, didn't you say you like the story in FFT better too? Isn't there a remake on psp! :D. 

offtopic. Do you think they should have not used all caps in Tactics Ogre?

infamous

bioshock

eternal sonata

1. Endless Ocean

2. Oboro Muramasa

3. Chrono Trigger