Calibre
Finally found some spare time to look into ePUB generation; the options include Daisy Pipeline, creating the ePUB from scratch, Calibre, and not doing it at all. After a little fiddling (and a little time off for a bug report and an update), Calibre is generating ePUB files on demand.
Manybooks is using the command-line script html2epub, which is just one small part of the Calibre arsenal – there are OS X, Windows, and Linux desktop applications that can create ebooks in many different formats and will help keep your digital library organized, too.