Apparently fanfiction.net has fiddled with their code again, thus making Fanfiction Downloader not work for the site. Hopefully Raimonds is working on the issue, but since I'm terribly impatient, I went off searching for an alternate program. Fortunately, I found a *fabulous* one:
Gaffer
I have to admit, I like both the ease of set-up (note: you'll probably want either the SimpleOneFile (black text on white background) or the AllInOne (light text on dark background) template) and the information on the output file (original link! word count!) a bit better than on Fanfiction Downloader. Plus, Gregory (Gaffer's creator) is continually updating it, which means that Gaffer works on a lot of popular sites and/or more recent sites (including TTH and Archive of Our Own). In short, Gaffer is awesome.
The downside apparently is that: "Graffer only works on Windows OS with .NET Framework 3.5 installed." I have to admit, I'm not 100% sure what the .NET framework is, but the program ran on my computer without me having to change a thing (and a link is provided for you to download .NET if necessary).
ETA: Apparently I neglected to explain what the program actually does:) Essentially, Gaffer downloads all parts of a story from a given archive and saves them using your preferred template. SimpleOneFile (which is my favorite) combines all of the chapters into a single file, strips out all of the extraneous nonsense (menus, style sheets, etc), and gives you a file with nothing more than plain HTML and the RTF content of the story.
Gaffer
I have to admit, I like both the ease of set-up (note: you'll probably want either the SimpleOneFile (black text on white background) or the AllInOne (light text on dark background) template) and the information on the output file (original link! word count!) a bit better than on Fanfiction Downloader. Plus, Gregory (Gaffer's creator) is continually updating it, which means that Gaffer works on a lot of popular sites and/or more recent sites (including TTH and Archive of Our Own). In short, Gaffer is awesome.
The downside apparently is that: "Graffer only works on Windows OS with .NET Framework 3.5 installed." I have to admit, I'm not 100% sure what the .NET framework is, but the program ran on my computer without me having to change a thing (and a link is provided for you to download .NET if necessary).
ETA: Apparently I neglected to explain what the program actually does:) Essentially, Gaffer downloads all parts of a story from a given archive and saves them using your preferred template. SimpleOneFile (which is my favorite) combines all of the chapters into a single file, strips out all of the extraneous nonsense (menus, style sheets, etc), and gives you a file with nothing more than plain HTML and the RTF content of the story.

Comments
I'll update the post to include this information:)
Thank you!
There are several bookmarklet options available there which will give you white text on a black background, and directions on how to save bookmarklets to your favorites folder so that you can use them whenever you wish.
(I prefer black text on white background, and use similar-but-different bookmarklets to give that to me--and I love being able to do that! Yay for flexibility!)
It's an awesome programm. Totally easy to use.
http://fanfictionloader.appspot.com/
I could not get the text section to work but the html and ebook worked fine.
If you use stanza on a ipod touch or iphone you can use the program to directly download the story into stanza. I tried this and it worked really well.
Directions at
http://sigizmund.com/reading-fanfiction-off-line-in-stanza-and-other-ebook-readers/
This site seems more up to date than the desktop program and I used it yesterday so it works with ff.nets new code.
Ooh, another program? I'll have to have a look in a bit :) And update my guide.
Did you ever check out the Firefox add-on I told you about?
I like the idea, though, and if you find another add-on that does something similar, I'd love to give it a try.
Hmm. It didn't dl them into separate folders for me. Did you follow the way I did it (on the guide)?
There might be something similar around if that one really didn't work for you. I could check.
I honestly don't know, then. Maybe it was the particular kind of site you were trying to dl from? I admit that I haven't tried it on all that many as yet. Or maybe there was a box somewhere that needed unticking :s
I'll have a look and see if I can find any alternatives.
http://www.home-eisele.de/index_e.php
To reach the DL-links simply click on "programs".
Works just fine. :-)
I depended on this nice little program. Has it gone the way of the dodo, or is it just a temporary glitch; does anyone know? I haven't been able to find out... :(
http://www.flagfic.com/
I've never tried it, but everything I've read about it is positive. Good luck!
It's not that I don't like Fanfiction Downloader - I was so satisfied with Graffer that I never even installed it. Checking the posts up thread it seems its now updated, so I will definitely try it out too. I think it's the new "share to social sites" link that's messing Graffer up, because it downloads story information, and cuts off abruptly at the word "Share". :headdesk:
And honestly, as long as the program covers the major Harry Potter archives, I'll be happy. After I spent years avoiding it because friends kept pushing it on me (a guaranteed way to make me dislike something intensely), I caved in recently and read the books, watched the movies, and I am now officially bewitched. I've turned into my friends. (Pot, meet kettle. :facepalm:)
There must be something about them, because there are some things there that I really didn't like but I'm reading fics like crazy! (Now that I'm here, I might check some of your recs; I wish there was a way to combine tags on LJ...)
I'm not sure if Fanfiction Downloader covers all of the HP archives, but I find that most of the HP archives have a Print feature that gives you the whole fic in a single file anyway. It definitely works for FF.net though, even with the new share feature (I just tested it to be sure:)
Have you read Cauterize, by Lady Altair? By the time I finished it, I was quite literally sobbing in my chair. I lived through a war in my mid teens, 14-17, dodging bullets and searching for food, and I'm very familiar with the emotional scars a war leaves on a person. While physical scars are avoidable if you're fast enough - and lucky enough - those are not. And Anna Fugazzi's The House that Cedric Built, for showing how they might rebuild and cope with the aftermath because I doubt very much that all is well in the wizarding world. It doesn't seem like they learned anything. Then again, neither have we, so... yeah. There's another disaster coming, I bet.
I'm off to explore the recs - I found out that it's actually possible to combine tags by adding a comma in between and appending this to the url:
/tag/tag1,tag2?mode=and