Hi, Doranwen,
I really like your idea of making epub versions of stories available. I've been reading fanfic as epubs too, using Stanza on my iPod Touch. I second everything Lynn S.M. says about Stanza. Fantastic app.
Your description of Sigil is intriguing. Just tried it. Wow! With the fields for editing metadata (title, author), it's nicer than desktop Stanza at creating epubs, in my limited experience -- but Stanza is aces as a reader.
Regarding your problem with line breaks, there's the Word solution others have described. You could also give the
Formatter page on the archive a try. It converts among fluidly wrapped text (as in your word processor), archive-formatted text and simple HTML. You can strip out the extra breaks using it. It'll work on stories using our current format, which has a blank line between paragraphs. For older stories that use tabs but no blank lines between paragraphs ... not so great.
Though when I opened an archive text file in Sigil, it knew what to do -- just like Stanza, it stripped the extra line breaks, and all paragraphs were fluidly word-wrapping. AND it did it for both old and new stories with their varied formatting. So, no tedious manual line editing or search/replace routines required. It thought the header block was one paragraph (like my formatter script does), but you can easily "press Enter" to restore the line breaks you do want.
Both Stanza and Sigil fail at poetry formatting -- if the lines of a poem's stanzas are single-spaced, they get word-wrapped into one paragraph. So poetry and song lyrics would have to be manually edited, just like the story header block.
There is one really nice feature desktop Stanza offers over Sigil: It lets you export a story in various flavors -- HTML, Word, plain text and PDF -- in addition to epub. It can even export to the mobipocket format, which Amazon's Kindle supports. (The Kindle, probably the most popular ebook reader of all, doesn't support epub, strangely enough.) Looks like Sigil saves as just epub. You might try using desktop Stanza for your intermediate conversions.
Since I'm going to do this for various fanfics, is there any way the Archive would want to host epub versions of fanfics as well? Should I post them somewhere online?
While I think it would be great to host epubs on the archive, the logistics will take some working out. Short-term, maybe a file uploader tool to let you upload your epub files to the server? Then maybe a wiki page you could edit in order to create download links? That would make them available to readers fastest. It sounds like bobbart and maybe others would like to contribute too. (Thanks, bobbart!) This could be a workable solution for all, though it may take some coordination to prevent duplicate stories being posted.
Long-term, we could put the epub download links next to the main story links in all the catalog pages. That'd take some time to pull off.
For a sample of what this could look like, see the archive's
Filename Z page. As one of the shortest catalog pages, it makes a great sandbox for testing. Aren't the icons lovely?

Just added the epub versions courtesy of Sigil -- they're the black buttons at the right of story titles. (Firefox is trying to open them if you left-click on them, but right-clicking and "saving as" works to download them to your hard drive.)
Filename Z is a prototype of what I see as the future of the archive: The site would be database-driven, with HTML the default story format, and text, OpenOffice, PDF and epub flavors (thanks to your suggestion) also offered. Maybe mobipocket too. But imagine nicer icons for the different story formats.
My nebulous hope is that if we feed a word processor story file into the future database, a magic conversion process will kick in, creating all these different formats. Getting to the magic part is what has me stumped. I've been plodding through PHP books, trying to wrap my English-major brain around programming logic. But it seems doable. OpenOffice format, for example, is basically a zipped XML file. Couldn't styles designated in an OpenOffice template match up with CSS styles for HTML pages, and even for epub docs too? Headline tag to headline tag, author tag to author tag, etc. And tools exist in PHP to manipulate XML documents and convert them to PDF and other formats. There's got to be a way, without doing it all by hand. If a story is properly tagged going into conversion, it ought to work. (She said blithely.)
An automatically converted epub, if that's even possible, would be missing the value-added features only a human could provide, though -- the chapter breaks, TOC and appropriate poetry/lyrics formatting. A bonus of going database, besides more powerful searching, is eliminating hand-coding. I suppose some will always be necessary. It's all hand-coded now.
Sorry, got off-topic.
I don't see as big an issue with it as with audio fanfics, or translations, but would there be permission issues?
Permissions in that authors' stories will be converted into a format they didn't anticipate, or permissions in that you'd like to host the files elsewhere?
I'm perfectly happy for us to host epubs on the archive, and I'm equally as happy if you'd prefer to post them elsewhere and have us offer a link to your page. But I'm fuzzy on if there's an implied agreement between the archive and authors about hosting their stories. When they submit a story to the archive, they know it's going on the archive. Would they be upset if it went other places too? Authors who happen to be reading this, would you object? And how about story formats: Would you mind if your story were turned into HTML, PDF, OpenOffice and epub?
A precedent may have been set for this years ago. Soon after Rhen's collection of FTP story files turned into a Web-based archive, someone out there in the ether created a mirror site. An Australian guy, I think. Nobody objected as I recall. Haven't heard anything of it in the last 10 years, so it's probably gone.
But I do remember we lost some authors and their stories in the process of going from a sheltered FTP site to a very public Web site. Because they were using their real names, they felt exposed. And for one reason or another, they were unwilling to adopt a pseudonym. One author -- Gail L. -- wrote a great story about Lois and Clark being stuck in an elevator for a few hours. I lost it due to a hard drive crash, darn it, along with all her other stories. Not that this last relates much to the issue at hand, other than that people sometimes offer objections you don't anticipate. (And I really miss stories when authors pull them off the archive.)
In the case of audiofics, as you say, it's a bigger issue. There was a thread where authors opted in to give their consent to have their stories recorded. But epubs are not that radical of a transformation -- it's still text you read on a screen, though more attractively formatted.
I'd say permissions issues are LabRat's call. (Tossing it back to you, LabRat! :p )
Thank you, Doranwen, for poking your head back in.

I think it's an exciting idea, and clearly there's lots of enthusiasm.
And thank you too, bobbart, for your interest and the Stanza how-to.
So what's the next step? I can start looking into a file-upload script and prepping a wiki page if that's agreeable. Or we can talk more and explore other options. I think it'd be good to hear LabRat's thoughts and see what our authors have to say.
Best wishes,
Lauren
P.S. I had to go to Wikipedia to find out who Rodney McKay is. Thank you for the comparison, LabRat, but I fall way short! He's probably more like bobbart, who can use a binary hex editor. How ubercool is that?