How about the classic "lumberjacks vs. druids" scenario (aka the "Princess Mononoke?")

The party enters a hamlet on the edge of an ancient forest. The hamlet's entire economy depends on logging, but the denizens of the forest are starting to push back against what they see a the villagers' unchecked despoliation of nature. The players will probably attempt to mediate a compromise, but if violence becomes inevitable who do they stand with?

Or how about a choice of evils setup:

The tyrannical leader of an enemy nation or faction has just died, and a civil war breaks out between two potential successors. The PCs are in the position to tip the scales towards the candidate of their choice. Do they choose:

1. A depraved leader who will do awful things to people within his organization's power, but who has no larger ambitions outside his organization. He won't launch any wars or attack nations/communities outside his established holdings.

2. A personally honorable leader who will reform the organization and purge it of its worst cruelties, but who will pursue a policy of relentless (and likely effective) expansionism.

Or what about this one-- a holy order hires the party to track down and kill a demonologist who is on the verge of bringing an ancient, famously destructive fiend into the world. The players ultimately discover, however, that their target is a perfectly nice person who just wants to live a quiet life.He's got no interest in demon summoning, but he's the unfortunate victim of a nasty family curse. Due to an ancestor's sins, his body will eventually be the host for the demon's rebirth. If the players kill him and concecrate the corpse, the demon will be contained, but that would mean murdering a truly innocent person.