There's this one part in Deus Ex where you make your way up a tower that has a fair number of UNATCO troops in it.
At this point in the game, they are your allies. Your goal is to send a warning message to the NSF (freedom fighters / "terrorists"). Once the message has been sent, your former supervisor sends a message of his own to you saying that he's instructed the troops below to kill you for being a traitor/failure. I tried to sneak my way out, but alas I was saving my invincibility cloak for a later segment and just resorted to shooting a few of them to death.
The next time I played through this segment (on a more pacifist playthrough), I used the electrical riot-prod to knock every UNATCO trooper unconscious on my way up the tower (they were still allies at this point) so I wouldn't have to turn the scene into a blood bath like I did before. However, this time the message I got was different. Basically the guy told me he "would have notified the lieutenant to give the kill order to the troops, but I see you've taken care of them".
I suppose that would be two small things.
Being unaware initially of alternatives, and then having the pursuit of an alternative path that wasn't immediately clear actually change something.