Since Calibre exports MOBI and ePub, they are the obvious alternatives.
MOBI support is good in FBReader, except that the cover image isn't displayed and, like all for all other formats, FBReader uses its own style conventions. There are a few other issues, like not starting a new page on section breaks.
EPub support is evolving. It used to be essentially identical to OEB support, and in particular it ignored all CSS and used its own global "styles". The latest version (0.10.X) includes "partial CSS support for epub files". I don't use ePub with FBReader much, but my impression has not been favourable so far. Of the two, I prefer MOBI but I am happy with FBReader's "global user defined styles" approach.
In any case, Calibre may be able to provide either MOBI or ePub based on the user's preference.
Another interesting option is FBReader's new
integration with network e-book libraries. This currently works for feedbooks.com, but it might be possible to integrate your own on-line library via Calibre. The same interface also works with feedbooks download guide.