Hope this is OK but as an illustration here's an excerpt from the GM chapter of my game Other Worlds which tries to make this stuff a big part of play:
Give the Characters Hard Choices
Now that the characters have both information and leverage, we get to turn up the heat and force them to make some hard choices about what they’re going to do. Many of these decisions will have a strong moral component, but some may be more personal or strategic in nature. Setting up these kinds of dilemmas can be a difficult part of GMing, but it is really the crux of successful play. Such problems put the character under the microscope and allow their player to make a clear statement about who they are and what they truly believe in. These statements then lead in to further character examination and development as we begin to explore the ramifications of what he has just done – and who he has done it to.
All the ammunition you need to create these moral dilemmas is right there on the character sheet. Take a close look at each character’s values as an individual – his goals, his flaws, his relationships, and his personality traits. Pick one of these values and try to find some way to test it. Pit it against one of his other values, or against the success of the mission itself. Force him to choose which one is most important to him, or at least to find out what he will do to try to maintain both values equally. For example, you might test a character’s Loyalty to the Company against his Do the Right Thing ability by having his employers give him some morally dubious assignment, or test his desire to Become a Jedi against his need to Avenge My Father’s Death by having the one person able to train him be the same man who killed his father all those years ago (testing also his Compassionate ability against his People Never Change ability).
You can also explore the intensity of a character’s individually-held beliefs by setting up situations where they may have potentially undesirable consequences, just to see how far he will go in trying to uphold them. Is there a line he will not cross, a sacrifice he will not make? For example, if he is Scrupulously Honest, would he lie to get himself out of trouble? Or to save his marriage? What about to get his daughter further up the transplant list? If he truly believes that The Ends Justify the Means in his undercover mission against the mob, what will he do to preserve his cover? Will he beat up an innocent man? Will he sit back and watch while an innocent man is killed? Will he kill the innocent man himself if necessary?