The Rachni Queen.

For those who haven't played the first Mass Effect game, there's an encounter on the planet Noveria with a species called the Rachni. The creatures were a menace to civilization and thought to have been wiped out. but the corporation Binary Helix found a surviving Rachni queen and attempted to raise their own Rachni army. In typical sci-fi fashion, this proved to be a Bad Idea, with the Rachni young going feral and attacking people at the research station. The protagonist of Mass Effect, Commander Shepard runs into this situation, and after learning about what Binary Helix is up to, is eventually presented with a choice. Either use the facilities containment system to destroy the Rachni Queen, or let the Queen go free.

Now, the Queen at this point converses with Shepard through a proxy, and explains that it was a misunderstanding between the species, and claims that the Rachni can learn to live in peace with other races.

So Shepard is faced with two choices here. Destroy the Queen and exterminate a race of intelligent creatures, or free the Queen and possibly unleash a threat upon the galactic community. There is no real right choice, simply the choice the player thinks is the right one. It's a great scenario, and possibly the best in the original Mass Effect game. "Did you kill the Rachni Queen or let her go?"

There's a lesson in there for GMs on interesting choices that don't have a clear correct choice.