They make people uncomfortable, to the point of leaving the circle:

I left the filk circle at "Bide Lady Bide" because being surrounded by people singing approvingly of a completed rape IS KIND OF SCARY.
...
The song that drove me out of the filk circle was The Two Magicians. What is wrong with people? Why is this OK?

And the answer is that it isn't okay. If you're thinking of singing this type of song, please reconsider. If someone else starts singing one, it's okay to ask them to stop. If someone else starts singing one and another person asks them to stop, support that person.

Our singing culture is a little weird because we sing lots of songs we don't agree with. We'll sing that it doesn't matter how bad things are because everything is just going to be wonderful in heaven, that the woman marries the man only after he has completed heroic deeds, and that stealing a ship and marooning its sailors is ok because they're Chinese. While I believe all of these ideas are wrong, and even harmful, I'll still sing songs containing them. Apart from the message of their lyrics, these are good songs, and singing their words is a way we understand past people who saw the world differently.

Consider books: stories can be full of overt racism, sexism, nationalism, and other ideas we reject, but still be worth reading for their other qualities or even simply to better understand the misguided ideas that led to their production. In both books and songs, selection is evidence that you approve of the message, but its only weak evidence.

Pragmatically, if people are interpreting your singing as approving of ideas you don't hold, and especially if that's leading them to fear for their physical safety, you shouldn't do that. But if we can keep song choices from seeming like endorsements, that would be better.

Update 2012-09-05: A friend writes:

I was going to write this as a comment but I'd prefer a bit of anonymity on this topic. I don't feel I know enough about the song BDan described or the context in which it was sung to make a judgment as to whether it was OK, but based on his description that they sang "approvingly" I'm guessing it crossed the line.

First, while comparisons to other "bad things" like murder and piracy can be useful, I think sexual assault/rape/abuse is a different class of subject matter than murder or piracy, in that it's much, much more common and tolerated in our society today. If you're singing in a group situation, there's probably at least one survivor of sexual assault in the room, and there might also be at least one perpetrator. I think it's much more likely that your favorable portrayal of sexual assault will reinforce rape culture (and thereby contribute to an actual assault, or make a survivor feel unsafe) than your favorable portrayal of piracy will result in increased piracy in your community.

That said, I don't think that any mention or allusion to sexual assault/abuse is necessarily bad or wrong, and eliminating those themes entirely would knock some great and poignant songs out of use. There's a difference between a serious song that tells a story involving sexual assault and a song that makes light of sexual assault. The former, sung with an appropriate degree of seriousness, is still about difficult subject matter and might be triggering or hard for a survivor to hear, but it doesn't make me personally feel unsafe. I don't want to speak for others on that point - my opinion is that the tradeoff of some discomfort for hearing the story of that song is acceptable. The latter, singing a song in a way that makes sexual assault a joke or "no big deal", would absolutely make me feel unsafe, and I believe that that's not acceptable.

I should note that I don't think it's as simple as coming up with a list of songs that are "acceptable" or "unacceptable". Context and the room's atmosphere likely play as big a role in the appropriateness of a song with difficult subject matter as the song's lyrics. Consequently, I think it's up to each leader to think carefully about the situation that they're in, the song they want to lead that mentions sexual assault/rape/abuse, and what the point of that plot element is. It's powerful subject matter, and you as the leader have the right to address it, provided you assume the responsibility of addressing it in a sensitive and respectful manner.