You can easily uploade multiple files per article -- audio and video files will work, for example. I haven't tried flash files, but I don't see a problem with that either. And of course, multiple HTML and/or PDF files can be uploaded per article. All of these files can be uploaded during the Layout Editing phase, as Galley files; they will appear as links on the ToC, in the order you designate from the Layout editing page.
Technically, you can link between HTML files. This becomes a little difficult, however, as OJS automatically renames the uploaded files to adhere to its own naming convention. If you were to upload a file called page1.html, it would be renamed to something like 27-43-1-PB.html. So the Layout Editor would either have to anticipate the about-to-be-assigned name and edit hyperlinks accordingly, or upload the documents and have the Journal Manager upload edited files through their User Home --> Journal Manager --> Files Browser.
I don't know what kind of team you have working on the journal, but this may be an area where writing a plugin would be of use, if you have the requisite skill. Let me know if that would be of interest, and I can give you more information on how to go about doing so.