One that I've used in a couple different games, but originally d&d, goes as follows:
I was dealing with a player group that was a little too "shoot first, ask questions later", so I decided to teach them a lesson.
They were all good characters, though not necessarily lawful. Anyway, they were hired to hunt down a priest of Seth who had murdered this Caliph's children. The priest had gone into the desert to escape the Caliph's vengeance.
So, the group begins following his trail, but he has some considerable lead time. His sacrifices to his god often take the form of making good people fall to evil ways. So, knowing that there are people on his trail, he repeatedly creates situations where good people are pitted against the characters, whether by misinformation tricked into fighting them, or by magic, or whatever.
The characters first kill a group of local soldiers trying to protect their village from what they think are criminal rapists/murderers.
Next the group comes upon the ruins of a manor in the desert. They encamp there, and at night, the manor seems to become brand new, with women moving about, weeping the fate of their master. The mistress of the house explains to the characters that their lord had been enslaved, and is held prisoner at a keep one days ride away.
The characters figure out that these folk are all ghosts of some form.
The next day, they set out, trying to gain time on the priest of Seth. After a day, they come upon the keep, and find fresh tracks matching the priest's entering the keep, but not leaving. They enter the keep, where the "lord" of the manor they left the day before, who, as it turns out, is also long dead, is essentially trapped in undead flesh, like a skeleton warrior, but still inately good. The priest, who has the object where the lord's soul is held prisoner, commands the undead knight to attack the group, and while they are dealing with the knight, he escapes.
At the end of the combat, the characters destroys the lord, who let out a shriek that fills the air all around the keep. Little do they know that not only have they killed a good man(and they would have known had they listened), but that his death shriek broke the spirits of the women that waited at his manor for him, who then became banshees.
They didn't discover that little fact until the next night, when they were trying to catch up to the priest, and had a number of banshees fall on them, nearly killing the group.
So at that point, the "good" characters, because of immediately attacking and doing little else, had killed local guards trying to protect their village, killed a lord trapped in undead form, and caused by this action the corruption of a number of benign ghosts, who they then killed with their spirits thus sullied.
Needless to say, their cleric was incapable of healing the injured group for a long time, their paladin lost his abilities, and the group learned to be much more cautious and role play a little more. In fact, it turned into a very good role play all around.
For the traveller game I'm getting ready to run, the basis right now is a system that has one higher tech planet(not precursor, just higher tech), and one present day earth tech level planet. The lower tech planet actually has some very valuable resources, and so the higher tech planet does what it can to maintain control without risking civil unrest, which they do by utilizing political puppets.
Anyway, the characters are from the higher tech planet, and are sent to assist one of those political puppets where needed, while reporting to their homeworld on his conduct. Aside from this, they are also collecting intelligence about resistance groups, and are ordered to seek out and question a man they do not know except by photo.
Little do they know the man they are supposed to question is also from the higher tech world, only her has ties with the resistance. They will not discover this until they are mid mission, on an op they organized where their hirelings are attempting to assassinate a leader whose power base threatens the puppet leader they represent. In the vehicle with this leader will be the man, and they will have to choose whether to give the go ahead on the assassination and risk failing their mission from their homeworld, or cancel the assassination attempt, hope there is another chance, but otherwise risk their puppet losing his usefulness, leaving them stuck on this world without proper support.
