In regards to your comment BrainDamage, I personally think the story category should be to put things in their proper place for people searching for types of stories, then the tags can function ideally both as a further refinement as well as kind of a quick and dirty "parse this for things you don't like." I myself often look at them to see if certain specific elements I don't want to read will show up and I appreciate the people who take the time to tag their stories that way. It's a great courtesy for writers to show towards their readers, I think. Of course, it's also a place that's often used to stick jokes and things, I'm guilty of that myself sometimes...
I wouldn't expect somebody to throw their gay Full Metal Alchemist incest story into Gay or Incest category instead of Fan-Fiction, though I guess they could if they want. Then if it's gay or incestuous, there are all kinds of ways to flag that: put it in tags, make it part of the title, make it part of the subtitle, mention it in the story's description, throw a note at the front of the story, put it in parentheses next to the branch of the story that is that way, whatever works.
Wicker, if your concern is stories where you just click into the first chapter and they start giving you details about the mom's boobs, then speaking from a practical standpoint, you definitely know what you're in for. Can't you just jump back out? You haven't done anything more than just click the first page of the story yet. It seems like if you're worried about running into incest when you don't want it, the more pressing issue would be investing time in a story and then running into the incest when you're a few chapters or more in.
I'd just advise writers to try to be as courteous as they can with those flags. And readers, if you're having trouble running into stuff you don't want to read, I'd recommend perusing tags.