The largest archive of fic's available for download I've come by is The PDA Fiction site. The site is no longer updated with new fic's, but you'll find a ton of (fan) fic's from a number of writers available for download in a multiple of formats.
If you can't make use of the formats available at PDA Fiction you can get a free reader that support a multiple of format it's called Stanza, and it's available for both Mac / Windows-pc and iPhone/iPad (download here) or you can download Calibra - a free software that will let you organise your eBooks, read a multiple of formats and convert files to and from a multiple of formats.
This summer The Athenaeum started posting a number of the fic's archived at the site in eBook formats too, but I don't think that the crew at The Athenaeum is working on producing more eBook's at the moment, but still if you are lucky your favourite fic's is available for download at The Athenaeum.
I've also found that Auxip.com offers some titles in an eBook format - The Rocketreader format - Auxip have left a link to a download of the RocketReader software, but I really can't recommend it - I never got used to the reader. Files in RocketReaderformat can be converted by way of Calibre.
The Royal Academy of Bards has also made a number of stories available in the RocketReader format, and has linked to the site where the reader can be downloaded.