Well I remember in Mass Effect 1
that in one sidequest, you find a guy who is essentially brain dead, but on life support. You have the choice to either cut off the life support and let him die peacefully, or leave him there. I found it very hard for some reason. Probably because I kept thinking, "But what if he's not brain dead? He might wake up! But what if he doesn't. I can't just leave him here on this ship that was just filled with enemies all by himself!"
And in Mass Effect 2....
Choosing whether to rewrite the Geth or not. I just couldn't make up my mind of what was the more ethical way to do it. I mean, in the end, I'm just undoing Soverign's indoctrination over them. But what if that didn't happen? What if they just left because thats what the Heretics simply believed? Who am I to take that away from them? But I didn't exactly want to kill them. Legion kept telling me that it wasn't as big a decision as it probably was, but I just...didn't know what to do. Ended up rewriting them.
And the collector base! That damn collector base! I kept telling myself: we need this base's tech, if not then we are screwed when the reapers come. We are just not ready for them yet. But then I thought about all the crap that happened on that base, and how many people had died. Would it be justifiable to use the base in spite of that? And the one telling me to keep the base is TIM. Now, I wasn't actually too mad when he tricked me into going onto the Collector ship since that helped establish the existance of the Reaper IFF, and I knew that deep down, he was trying to save humanity. But still, that doesn't mean I trust the guy. I mean, what plans does he have for the base? Literally stopped for about 10 minutes to think about this decision. Decided to destroy. Thank God too. After seeing TIM's evil smirk in the Renegade ending, I was very relieved I made the right decision.
Felt a lot of the sidequests and stuff in Dragon Age 2 though made me uncofortable too. But thats probably because your choices are just so very grey, in a city were everyone is freaking crazy. Damn mages and Templars. Course it just becomes worse once you realize that your choices don't really impact the plot at all, so it feels like eveything I did was for nothing.
But for me, the most recent one has got to be Nier. I beat the game once, and I have a firm understanding of whats happened.
Then I play the game again, because now there are more cutscenes to explain the story even futher. And my God. What I found out what I was actually doing? I just kept saying to myself, "I'm such an asshole. My God why don't I stop? Why don't I stop?!" Then you take the ending(s) into account, and it made me feel so much worse. I didn't want to keep playing, but I knew I had to. Even after I would shut that game off, I would be saying, "I can't believe I just did that" for a good couple of hours....
Good game though! =D