If you’re using InDesign CS3 to create ePub documents then you’ll want to make sure you’re using the 1.0.1 update. The update includes an option to embed the fonts in the document and to use a TOC Style from the InDesign document, but more importantly, the update implements the OPS 2.0 v. 0.984 Draft specification (dated 16 Apr. 2007). The original export plug-in implemented a previous version of the draft, so you’ll want to get the update.
If you’re already using the update, you’ll see a faint ‘1.0.1’ in the lower right hand corner of the export dialog. You’ll also see the option to embed fonts and a third panel in the dialog. If that ‘1.0.1’ is missing, then you’ve not installed the update.