Believe it or not. After playing countless RPG games. I have came to my final conclusion of what I think had the most touching story. It is - Dark Souls: Prepare to die Edition.
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Spoilers below---
You're probably thinking, why on earth I chose dark souls, it's just a game designed to be hard and make you mad.
Well, first of, you are "the chosen one" - The one who succeed lord Gywn. Many other undead think they are the same and have embarked on the same quest.
Now, your story line isn't really the touching part of it. It's everyone you meet. They are all on their own stories, which you kind of shut down.
Solaire of Astora - On his journey to find his own personal sun. Although, upon finding it (The bug helmet) you either have to kill him and take the helmet, or steal it from him and he will forever be searching for that.
Quelaag - The chaos spider you fight, you kind of kill her sister off aswell.
Quelaag is half spider / half chaos witch, a lot like her sister(Which is hidden under the lair behind a secret wall). However, her sister doesn't know she is dead(if you equip the old witch's ring, you can hear her speak). So she thinks you are her sister, even though you just butchered her a few seconds ago.
I think Quelaag was just trying to protect her sister, by hiding her behind a wall and feeding her humanity of those who she killed.(When you feed her sister humanity, it eases the pain she is in)
Sif, the great grey wolf: Although he appears to attack you at first sight just because you looked at it funny, it's because it's his master's sword, the person who saved his life. I felt really bad fighting sif, A) Because I love dogs / wolves and B) When he's low on health, he limps around and makes a whimper
If you play with the DLC for the game, and go and save sif and equip the shield he gives you when he's a puppy and then go and attack him, you can tell that he really doesn't want to fight you.
This is just some of the reasons why I love Dark Souls and cannot wait for Dark Souls 2. The game just looks like a dungeon crawler, but has thousands of great lore behind every character.