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[For XHTML markup, one thing that comes to mind (just off the top of my head) would be to enclose all the text that makes up an original page with a surrounding tag that uses the "id" attribute to hold the page number. This would not display, but could be accessed if needed. Also, by using "id", you could construct a special hyperlinked table of pages that would allow you to jump to specific pages in the ebook. I'll have to try this and see how it works.]
Some such solution might satisfy everyone. Current scholarly journal databases such as Project Muse give the page numbers in square brackets within the text--an "ugly" solution, I suppose, but a simple one. JSTOR, the dominant archive of scholarly journals takes a different tack. It uses searchable PDF files and presents a scanned graphic representation of the original journal page, so the pagination problem is not an issue. However, the downloaded PDFs don't look all that great on the Sony Reader, though they are usable.
Sorry to have caught up with the conversation so late; I don't get a chance to log on to the forums every day.
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