I think the best choice is using the actual page numbers from an existing book, like the Kindle does with books for which that's available. This has the advantage of allowing comparisons between different brands of e-readers as well as physical books.
For e-books where there is no physical book to refer to, my preference would be for some sort of normalized "paperback page equivalent" based on word count. Although since most novels chosen at random from my shelf have about 500 words per page, I'd prefer that number, since I'm extremely familiar with various differences between paperback books. As I'm sure most people on MR are - if I say that a book is 200 pages long, or 350 pages long, or 550 pages long, most people who read will intuitively know what that means.
Digital cameras do something like this - if a digital camera says f3.5-6, they are usually giving you the 35mm equivalent, since that's what people who care about f-stops know; the *actual* numbers for digitals are meaningless to me.
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