Mind you, it's of course possible to avoid reading something that squicks you because the pairings are labelled. (For example, when I see something credited with Noah/Claire, I definitely won't read it because the very idea grosses me out. So does Sylar/Claire, for that matter, but that's another squick.)

Yes, absolutely. I think people are doing really good with that, to the point of erring on the safe side (I mean, labelling Peter/Claire as "AU, canon incest" is kind of factually wrong, even though I know what the author wants to convey.). It's more the reaction in discussions - I remember a conversation between kattahj and me about feeling squicked out by Noah/Claire, and we both felt compelled to make a disclaimer about people having a right to their kinks (hugely paraphrasing here). I felt weird about that, because I have a huge problem with that specific pairing, but at the same time I had (and have) the impression that voicing that opinion is frowned upon in fandom, because it is seen as oppressive, or taking away people's fun. There's a bit of peer pressure at work here, probably. (And, as you say, it hugely depends on the fandom: I haven't seen that much Adama/Apollo fic yet. At the same time, I definitely feel sorry for any SPN non-incest or - shock! - gen fans. Of course, the latter might be the fan equivalent to Nessie.)