Oh, this isn't quite on topic, but you know how in FF Tactics, if you want the good characters later on you have to let some old ones go? Well, I'd go through the process, and see what the goodbye dialog was like, and cancel and redo until it was a happier ending (like, bittersweet instead of just depressing). So that way I felt like they were moving on, to do something equally fulfilling, and not just getting dumped.

I felt bad when i made some dude open up a pipe full of poison in infamous so i wouldnt get infected lol

Killing the little sisters in Bioshock.
D:

You just felt bad cause you wouldn't hear Sasha talk to you!

i hate some things i have to do to get the platinum trophy for Heavy Rain

When I used to put herbivores in with carnivores in zoo tycoon to see what would happen. Oh and making roller coasters in roller coaster tycoon that would jet off the track exploding into a million pieces killing dozens of people. I was a monser..... :(

Agree with you about Shadow of the Colossus, especially with the music they put after you kill each one.

Right now I can only think about GOW3 and Fallout 3. GOW3: Pandora and Poseidon's mistress. Fallout: letting the Ghols inside Tenpenny and slaving Red.

Let's see, off the top of my head:

Beating extortion money out of people in Godfather. They're just business folk trying to make it in New York, and then I show up and trash their merchendise, shoot them in the knee, throw them through a window, and demand that they pay me for the privilige.

In Knights of the Old Republic, I killed some ancient, mysterious beastie that was the source of a magical healing substance called 'bacta.' Sure, it was being monopolized by the bad guys, but that stuff had saved who knows how many thousands of lives! Not anymore.

MadWorld. The whole game.

In Bully, I helped the ogre of a lunch lady date rape one of the teachers. Aside from the physical and emotional trauma, who knows how many diseases I helped inflict on that poor man.