The Kindle has one feature that the Nook does not have: Electronic delivery of personal documents. You can't email a word doc or PDF to myname@bn.com and have it converted and delivered to your device. You have to save it from a computer, convert it, plug in the Nook, and copy the file over.
For book readers that might not matter. But it can be pretty attractive if you go beyond reading books by using something like Instapaper to "bookmark" articles throughout the day, then have them all automatically on the Kindle.
This can be the feature that makes a huge difference once you start to use it.