I briefly considered trying Stanza, but I don't have an iPod Touch or anything of the like, and I couldn't figure out where to download it. I'm also not fond of anything too Mac-centered (I actually figured out how to install just the necessary files for my iPod Nano to communicate with my computer without installing iTunes itself, which is a memory hog on Windows and not a program I want at ALL--I'm using foobar2000 to manage my iPod library instead).
I poked around, and ended up going with Sigil, which had such a shallow learning curve that I've got one children's book converted and am working on a second, in about two days' time, TOC and all. I haven't tested it on the fanfics yet, but I plan on editing those line breaks in the txt file anyhow so I don't have them hanging around all uglified. If I try it in Notepad++ or some other Notepad replacement, I hope to be able to do some better search&replace, since Notepad won't let me replace boxes with carriage returns.
Can read stories in many formats, including PDF, plain TXT, Word documents, etc.
The Astak EZ Reader can read a whole lot of formats too, actually--that was a big reason why I wanted to get it over other e-book readers (price was the other one)--but not all of them have all the features. Some you can't search in, and a lot of them don't have a TOC or anything like that. PDFs are close in features to epubs (though some look atrocious due to the nature of pdfs), but epub is better than the rest because it has search, TOC, and more zoom levels altogether. Txt format is very limited on the Astak EZ Reader, so I would need to convert to something else if I wanted to take advantage of any of the possibilities (TOC would be nice with some of the gigantic novels--I can't imagine trying to read Masques, for instance, without some sort of chapter system--what if I wanted to just read from a certain point on?). Epub is a natural choice because it's the best-supported format on the Astak, and Sigil is an easy program to work with. I can make sure it will look good and be formatted nicely when I'm done.
