The difference for me was the native support, including DRM protected ePub files. All the books I have downloaded from Barnes and Noble have been ePub so far, and they are using Adobe's DRM system. This allows me to keep the books I've bought even if I decide to buy a Sony reader, or a number of other devices on the market as well. The Kindle seems to only download books from Amazon in their proprietary AZW format.

I can definitely see the appeal of the Kindle prior to the Nook's release though, and nearly did pick one up. Long term, I hope ebooks move to a standard format across the board. Sony moving from their proprietary format to ePub was a big step in helping that to happen.