One simple example was when I was told to meet a certain contact down by the docks to help me break in to an area. Well, I forgot to do that and got in on my own. Later, on the way back, I saw where the guy was and went up to him to see what he'd say. I figured he'd either say nothing, or give me the canned "I'll help you get in" speech that was now useless. Instead, he chewed me out for not showing up earlier! That really cracked me up.
After that, I often tried doing weird things, and usually the game had some kind of humorous response. It was great.
Beware, though, the game does not seem all that cool at first. For the first few hours of play, I thought it was just an extremely difficult Doom clone. That's not what it is at all. It is a very deep and detailed shooter/RPG/adventure game. Also, don't even think about playing it on any difficult level below "hard." If you do, you will miss out on what the game is all about.