Journey.

Not part of the story but kind of a spoiler, so look away if you've yet to play the game but want to...

... reaching the top of the mountain and having this player who I'd been on this epic 2 hour journey with draw a heart in the sand as we said our goodbyes.  Bloody hell.  It was an emotional sucker punch that I genuinely wasn't expecting and it really upset me, but in a good way.  I found the guy's name afterwards (it was in fact, a girl) and sent her a message to say thanks.

I would say by far Mother 3! and this even though I was reading some translation on gamefaq while playing in japanese. Not only the plot is very emotional, but the whole story is like some sort of critic of our society. The way I understood the message of this game was like the way we treat our natural environement (the pigs army with their manipulation of living species and New pork city) and the people we love is leading to our own destruction unless we come back to what make us really human.

Anyway, anybody played that game/ felt the same?

The sunflowers field was probably one of the most emotional moment in gaming

Final Fantasy VII

SMB. That first goomba was epic story.
FF2/IV comes close second.

All the Mass Effects, FF9 and Tomb Raider.

Mass Effect mainly because of my love of Garrus, Ashley, Mordin, Legion and Thane. In ME3 I was annoyed when Ash got wounded and so returned to the Citadel ewhenever I could.

My god the games people are listing are ridiculous, Uncharted 2? Is that a joke....Tomb Raider 2013!!?

I'll have a go...

Phoenix Wright series.
Layton series.
Chrono Cross
Eternal Sonata
Star Ocean Till The End of Time
Chrono Trigger
Phantasy Star IV
Resonance of Fate

Majora's Mask, i love the feeling and atmosphere in this game so much.

Red Dead Redemption's story was just great. Arguably the best game Rockstar ever made.

EDIT: lol, i forgot the first Knights of the Old Republic. Man, one of my absolute favourite RPG's.

Final Fantasy VIII - I really felt Squall's plight about being an orphan and I felt that he really loved Riona. Awe man and at the end of the game I was hoping that Squall wasn't dead. Best Final Fantasy ever and best emotional game!

You need a girlfriend.

Ash is by and large a selfish ignorant character in ME3 and far from likeable :p

FF9 though much respect :)

Gotta agree there.