After more experimentation, the best way I've found to format non-drm'ed books is the following:
Open the file (rtf, htm, txt, lit, etc.) in Book Designer and create a table of contents. Save the file in Sony Reader format. Add that to Calibre and output the epub file for Bookeen Opus. You need to remove lines after paragraph (an option in Calibre). I also find the text easier to read if the line size is set to 20. This process enables font selection and TOC. And you can change some other things (e.g. margins) if you wish in Calibre. I bought the opus because Frys had it for $149, and thought I'd probably return it. But it's grown on me -- the size, feel and design of it are quite nice.
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