Only game to ever successfully tug on my heartstrings was Bioshock: Infinite. The story itself is good, but the ending kept me up that night.

Can't believe no one mentioned the last of us yet. It's the only game that made me jump from an emotion to the other instead of the usual "ok... sure thing virtual world".

EDIT : Oh, two already mentioned it, that's a bit more believable. But still, you don't deserve gaming if you consider any game as touching/more touching than the last of us! How dare you?

Assassins creed 2 (when his family dies)
Halo 4 (when cortana dies)

*_*

cookie clicker

the walking dead... I cried

Battlefield 3 when u get knifed or knife somebody, their eyes look like they are about to cry, i know this isnt the story line but you should check out some battlefield knife montages. Look into their eyes as they get knifed...you can kinda hear how they feel at that moment.

Final Fantasy VII - VIII - X

And...

Dark Souls (Artorias and Sif, dam u ;_;)

Couldn't agree more on final fantasy. FF X, I cried like a pussy.

I couldn't agree with Faint and kris more on this. I always find myself calling someone a son of a bitch while forcing myself to man up.

Kain for switching teams in final fantasy IV

Garbanth for betraying Basch in final fantasy XII

Vivi finding out he was an artificial life-form and then going into a deep depression in final fantasy 9

but by far the biggest tear-jerker was when Auron finally got sent because you knew it was inevitable after finding out he was an unsent, I immediately went to the net hoping for an optional ending hoping he could be saved.
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Also yes the ending of bioshock infinite was masterful to say the least.

The ending of the first fire emblem released on the gba when the dragon he slayed was actually the woman he loved tugged on the strings.

Its so sad that there's no game actually touched my heart.
So I'll just say FF series before XIII