O'Reilly's Got Bookworm(s)
To my shame, I'd not come across Bookworm before:Bookworm allows readers to add ePub books to their online library and read them on their web browser or mobile device. If you have a portable device that supports ePub (such as the Sony Reader or iRex iLiad), you can download your books to put on your e-reader. Bookworm is specially optimized for use in the iPhone and can export directly to Stanza.
More to the point, it's open source, available under the BSD licence (and thus suitable for all commercial use, too).
Bookworm is now under the aegis of O'Reilly books, which seems appropriate. It's a good time for the project to receive more resources and a higher profile: ebooks are beginngin to take off, and it's important that there be a free reader that can benefit from that, and that we in the free software world can support.