The ideas mentioned in here are great and a lot of what I would suggest. I like throwing curveballs at my team, because it makes them think. Too many times do people create a run and everything goes off without a hitch, they shoot stuff and get away. At least in the movies, sometimes in the video games.
Combat is a distraction, it is a filler in the movies and games, because they needed a way to expand the game and add challenges for the player. I am not knocking combat; I play FPS games, I play RPG games with their random encounters. However, I do love the Ultima series.
For those who haven't played the Ultima series, the first three games were your standard 'Go here, fight this guy and save the world. Oh, by the way, kill all these monsters on your way'. After the third game, Richard Garriot was getting a lot of feedback about the immoral actions in these games, like stealing and killing all the innocent villagers, and decided to shift the focus. He then created the virtues and in the fourth game, it was the quest for the Avatar, an embodiment of these virtues. They were based off Truth, Love and Courage, in different combinations, forming Honesty (Truth), Comassion (Love), Valor (Courage), Justice (Truth/Love), Sacrifice (Love/Courage), Honor (Turth/Courage), Spirituality (Truth/Love/Courage), Humility (None).
The player had to try to live up to each of the virtues in all of his actions, which sometimes meant having to go out of the way to do things and prove yourself worthy. For example, to cast magic, you needed to use reagents which you could buy from shops. One of these shops was run by a blind man. You could buy as much as you wanted, and as long as you paid a couple gold, you would get away with it. But you lose honesty for doing that, and then you have to make it back up. If you run from a random encounter, you lose valor, etc.
So, one example the game system had to determine what type of character you start playing as was a quiz. You can find an example
test here. It was full of hard moral choices for people. Might not work much for Shadowrunners, but some of t he choices in the test and in game make for choices that could put the palyers to thinking.
They put the player in a room with all sorts of switches, gates on all sides which opened to rooms with more gates and so on. Each switch changed the state of some pattern of gates, and the object was to open a path to the exit. In some rooms were feral children who would attack the player's group. You could kill the children, which hurt some virtues, but you didn't deal with them attacking after that. Someone even tenured a resignation because they didn't want to work for a company that supports child abuse.
But as Richard Garriott said in an interview: "They could reload the room and not pull the lever; they could put the children to sleep and walk out; you could charm the children and make them walk away; they could drop their weapons so they wouldn’t hit them and attack them until they went below a quarter hit points and the kids would run away; they could use a fear spell and make them run away, etc. There are lots of options that don’t involve killing children. But the point is, I provoked an emotional response, and that’s so hard to do in games that I was proud to have done this."
Anyway, just putting characters in a lose-lose situation is definately a great way to do it. The problem is trying to get the connections required to make things work. The death of Spock in Star Trek films to save the rest of the ship was a sacrifice he was willing to make because he was saving his friends and many innocent people. PCs don't usually get that connection to virtual people, so what you need to do is come up with some terrible options either way; think the Train Job episode of Firefly; if you do the job, your reputation will be showing you as a heartless jerk and certain contacts will no longer associate themselves with you, but you'll get paid, and if you choose B, you will make an enemy but you'll still have your reputation.