A reader on Twitter just asked me how I protect my work, and the answer is too long for a tweet. Actually it's not, because the short answer is that I don't really do anything. There is an implied copyright just by posting to a blog (anything you post originally online) and while it's weak, it's fine for me right now.
In the past I have had an article I wrote reposted somewhere else without my permission although the byline was intact. I was furious at first, but then it was an article that helped people understand science (the difference between theory, hypotheses, and laws), AND it was being reposted in a place that was more accessible for school children AND I was no longer getting royalties anyway, so I came to the conclusion of 'meh'.
When I worked in non-fiction publishing, occasionally some of our more popular ebooks would come up on the black market in countries that had poor access to book distribution (I'm looking at you India). We were well aware of it, but we had absolutely not recourse other than a sternly worded email perhaps, and certainly not the funds to try to shut the pirates down. It was just something that was accepted as a loss. It happens.
As an indie writer though (and where so much of my stuff is available gratis), I'm not particularly concerned about it. If something I've written pops up somewhere it shouldn't be, I'll be writing sternly worded emails. If someone writes something derivative from something I've written (i.e. fanfiction), I'll probably just do the Snoopy dance and consume a celebratory hot chocolate, because to me, that's a fantastic milestone on the way to being a 'real author' *in the voice of Disney's Pinocchio* (I already am a real author, I swear. I'm traditionally pubbed in non-fiction. Also, I'm listed on IMDB. I've got street cred. Not much, but I've got it. And besides, indie authorship is real authorship...I'm not being neurotic).
The only thing that would really bother me is if someone passed off my work as their own. Since the market for short stories is astoundingly terrible, I doubt anyone would bother to do this. But if they somehow succeeded, I'd resort to a sternly worded email. If that fails, I will hunt down their mailing address and send them as many mail order catalogs and unpaid magazine subscriptions as I can find until I reach a satisfying level of catharsis. And then I'll send them a few more.
Seriously though, I have used the WGA to register stuff in the past (mainly screenplays I was trying and failing miserably to get agented--they will only accept stuff that is registered by the WGA). It's relatively cheap, and I'd be willing to do it again for any longer length stuff (including novels). Another option is using a notary, but registration is actually easier because it's all done digitally online.