Oh yes plenty of times. In fact it's a wonder how I even manage to complete the Dark Brotherhood questline at all.
I remember once I stole some coin purses from Honorhall... Immediately I realized what I had just done. I tried storing some gold in a chest but I couldn't. So I looked through my inventory and saw a gold diamond ring I had crafted earlier. I dropped it and placed it on the pillows... and when I couldn't see it I decided to place it on the nightstand. I figure if they need a little extra gold they can always just pawn it. That or that one chick might just keep it and let the kids starve. Either way my concious was clean.
Killing Nilsine. Now I knew that if I did this optional part of the quest that Tova will commit suicide. In fact I was looking forward to see if you can find her dead in her house. When I saw the body and read the note... it sorta hit me.
I pretty much destroyed the Shattershields. The father is now a complete drunk. Both his daughters are dead, one of them at my hands, and his wife commits suicide. To make matters worse the family war hammer has been stolen... which I may or may not have reclaimed and if I did... well it's in my chest in Breezehome.
Taste of Death... yeah. After eating the poor bastard I quickloaded and redid that part and just killed everyone. That and it broke my whole no cannabalism rule.
Sometimes I feel guilty over abusing the horrible AI. But not always.
Oh and stealing from Carlotta or whatever that chicks name is with the kid in Whiterun. I did it anyways and again I may have left some gold and or valuable items to replace the jeweled stuff I stole.
Oh and then I felt bad about killing the Old Orc. Well not so much killing him. But so much that I interfered with his Good Death. I mean seriously 2 Werewolf Skinwalkers and 3 Frost Trolls. Pretty sure that would have done it. After the rather fun battle the Old Orc's health wouldn't regenerate. I had to make sure he had a good death. So instead of taking advantage of the 1 hit kill I let him beat me almost to death. Oddly enough it's harder then you might think. Well the way I play anyways. But in the end he had one gloriously epic fight together and gave him an honorable and good death.
While I had no actual part in the Farmer's wife dying. I did feel bad for him. He came up to me in anger and started beating up on my old horse blaming me. I think he was. Shortly after he came up to me he turned into a werewolf... So I killed him. No guilt over that though.
Then this one time at bard camp...
But I'll tell you one thing I am not nor will I ever feel guilty about. Soul Tearing a Giant... and then watching as that Giant sent the other giant to the moon. Best. Moment. EVER. Actually the old orc, farmer, and the giant all happened today. So glad I decided to check out something while on my way to blackreach.
Hmm... I am sure I have plenty of other stories to share.
Oh Black Soul Gems.
Seriously after visiting the Soul Cairn... I just didn't have it in me to use all those Black Soul Gems with grand souls in them. So i sold them off. I almost swore off enchanting altogether. Luckily I talked to Serana or whatever and she mentioned it's probably only the black ones...
So there you have it.