Update (as of 16 November 2012): these instructions still work for the iOS 6 and iBooks 3. Happy downloading!
I’ve always thought that this bit of functionality was common knowledge — the internet, after all, was made for pr0n. I was apparently wrong when I got a million questions (okay — I exaggerate) on Tumblr, asking how I managed to get a library full of fan fiction from An Archive of Our Own Dot Org (aka AO3) on to my iPad. So!
Here’s a quick and dirty how-to on storing fanfiction in your iPad as e-books:
First, download the iBooks2 app from the Apple App Store — this app is the one developed by Apple, accept no substitutes. Next, surf on over to your favorite fanfic on A03. On the upper right hand side, there is a button that says Download. Click that and you will get a pull down bar with a number of download choices.
Click the EPUB button, and you will be taken to another page asking you which app to use to open the file. Select iBooks, and the file will automatically be saved to the app and stored in the app’s library. You can customize your bookshelf somewhat by storing groups of fics in separate shelves, however I have not yet figured out if it’s possible to customize book covers to suit your tastes (they appear to be random).
That’s it — have lots of steamy offline fun now, y’hear?!