I know you have probably have written articles about this but I don't really pay much attention to Amazon and eBay fees because there is not much you can do about them, but I just compared the fees for a $11.95 book on both, and the way I see it, you pay just about twice as much on Amazon now, if you offer free shipping on both sites. Amazon is $3.59, eBay is $1.73.
This does not include listing fees on eBay 10 cents (or free with a store) and Amazon's monthly fee which is $40.00 and eBay's store which is $75.00 (for 1000 free listings).
So I guess eBay will see a huge increase in book listings in the near future, books will not sell as fast on eBay but I would guess the selling price on eBay is higher that Amazon about 70% of the time due to high competition on Amazon.
Note from the Editor: Amazon changed its fees in the media category effective March 1st, which you can read about on this November 10th EcommerceBytes Blog post. Are you seeing the same impact as this reader?