I realize that not all of these qualify as true rat bastardy. Some of them are more in the other category, but they're all pretty fun.
***Wow, that's alot longer than I expected.
My personal act of rat bastardy was an entire Star Wars (WEG) campaign. Set during the Tales of the Jedi era, it involved three worlds (with no space travel) linked by Force created hyperspace tunnels, an Ecchlesiarchy, a Feudal Society, a race of tribal slaves, and an ancient Dark Jedi. I had two different groups of 6 Jedi PCs running through it simultaneously, occasionally meeting up together. The consequences of one groups actions often rippled across to the other.
I think the best part was when two of the PCs discovered that the Priests of the Ecchlesiarchy viewed the Force from a "balanced" perspective. They pointed out that the Force is a manifestation of all natural, living things and that anger is a natural emotion. They slowly eroded the intellectual difference between the Light Side of the Force and the Dark Side. Then, they informed the PCs that they had found a way to "cleanse" themselves of excessive Dark Side energies. All they had to do was engage in "communion." Communion involved the consumption of a small wafer of a spongy material. After they did so, the one character who had a Dark Side point discovered that it had gone away.
Subsequently, they discovered that the wafer was the flesh of the ancient Jedi (who had been corrupted by the energies of the Dark Side and now lived in zero-g in a space ship hidden in a nearby gas giant). By eating it, they gave him access to their rage and hatred (making him more powerful-- everytime they used a Dark Side power, he got the Dark Force point). Furthermore, when the other team eventually took a lightsaber to one of the priests, they discovered that long term exposure to the wafers slowly turned the user into the same type of material.
Of course, since the Dark Jedi was powering the hyperspace they couldn't just kill him outright. If they did so, the billions of people on the city world and the entire tribal race on the desert world would die. While the nobles on the agrarian world were okay with this scheme, the players really weren't. Eventually, they discovered that the tribal race's elaborate ritual prayers were actually the piloting techniques for spaceships hidden under their world's sands. Of course, they still had to convince the former slave race that transporting food and supplies between the worlds of their oppressors was a good idea.
Eventually, of course, the heroes negotiated an agreement between the nobles, the former slaves, and the lower ranking (and not outright evil) priests to establish a short term government until the Republic could send diplomatic aid.
Other good acts of rat bastardy that I've had the joy of observing was the GM who was running a Mage oneshot where the PCs were either Technocracy agents or Tradition mages working together under duress to investigate a Technocracy construct in Seattle that had dropped out of communication. The party didn't know it at the time, but the head of the construct was a barabbi (a Mage allied with the Nephandi (mages allied with the forces of evil and corruption ala the Great Old Ones and Demons)) and was working fully for his true masters.
Like I said, no one in the party knew what was going on. Not even at character generation. I took the GM aside and asked if I could play a MIB (man in black) barabbi. I played the character pretty straight laced, with sadism as a flaw (I gratuitously broke a mortal NPC guard's arm). Since most of the party were Tradition mages, everyone chalked my brutality up to my being an MIB. At one point, the Tradition mages split off to deal with one problem, leaving myself and the other Technocracy mage alone. At this point, the head of the construct contacted us . . . imagine my surprise when I discovered we were both playing for the same team.
I convinced my partner not to interfere with us and then lured the party into a trap. Since this was so totally unexpected, the GM allowed them to escape, but in my book this could easily have been a TPK.
Finally, while playing a published adventure with the D&D logo on it, we found ourselves up against a monster with DR xx/+2 and no +2 weapons. We needed to have an NPC draw the blood of a demon. We caught the demon, stunned it, but the NPC couldn't do enough damage to hurt it. Eventually, the demon woke up, ate the NPC, and turned invisible. Then the watch arrived. We were tried and convicted of murder, forced to pay for the NPC's raising, we had to pay him 5,000 gp in restitution, and serve a sentence of community service measured in years. It could have been worse, but we presented pretty convincing evidence that we were actually in the process of saving the world, so they geased us to return when we were done. We later discovered that the weapon we needed was in an appendix . . . but not included in any other part of the adventure.
In the same series, while infiltrating a castle full of gnolls, our cleric made a mistake. Although the adventure had been written to take into account that a party would have to fight its way through the gnolls (it stated that the gnolls were used to fighting in the halls and that the sounds of normal combat wouldn't bother them), our cleric (who wasn't really all that bright) decided that he needed to use a thunderstone to stun a group of bad guys. The DM ruled, quite rightly, I believe, that the sound of the thunderstone was not "normal combat" and we suddenly had 82 gnolls attacking the party.*
--G
* Fortunately, one member of the party was actually a polymorphed wyrmling silver dragon with a few sorceror levels (he told everyone he was a sorceror/monk . . .) and picked this moment to reveal his true form. His paralysis breath weapon and some good rolls kept the party from dying.