For Stanza, there's really only two choices - eReader and ePUB. I've mostly tested ePUB because Calibre couldn't convert to eReader before.
ePUB is supported well enough, I guess. Table of Contents work, but is displayed in a flat view, iirc (for multi-level ToCs). Stanza, however, purposely doesn't display some styles. Actually, the settings override the styles in the ePUB. For example, I've only gotten text-align:center to work when inside tables.
I did make a purchase of an eReader ebook (fiction) from Fictionwise and I don't really see any difference on how Stanza handles the two.
ePUB would probably be best, though, seeing as it's an open format and is basically a zip file containing html files.
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