FanFictionDownloader.net

http://archiveofourown.org/ is a new fanficton site with an open beta. It currently has 7370 fandoms and 227620 stories, making it eligible for inclusion. Plus the site has a bunch of different methods of sorting stories, and is much more upload friendly than fanfiction.net.

Sample links:

http://archiveofourown.org/works/87602/chapters/118649

http://archiveofourown.org/works/139898/chapters/201047

http://archiveofourown.org/works/164010

I'd never heard of this site before, but now I'm glad I have. I love how it's non-profit, and it has some nifty features. I second the request.

Yeah, it's new, and I hate how half the stories feature a celebrity!

but...

All in all, it's terrific. Its editing and upload capabilities far exceed any other site that I can think of, and it has few requirements on layout (Hooray, I can indent my paragraphs!)

It looks like archiveofourown.org has it's own download system that includes ePub and html so calibre could convert it to whatever you need without adding it to FanFictionDownloader.
Not that it's not good to have it just that adding sites without a native download system may be a better use of time.