After playing with both I went with the Kindle. Although, my library's ebook selection is zero so I didn't have to take that into account.
The Kindle user interface is so much easier IMO. Looking up words in the dictionary or googe/wikipedia is much easier and faster with the kindle. Taking notes, underlining passages and actually finding those notes/underlined passages is also easier on the Kindle afterward. I was able to pick up the kindle and use it without any instruction, where as with the Nook I kept having to ask my friend how to do everything.
As for the number of books; when you take away googlebooks and public domain books (Which both have available) Amazon's ebook store has more than B&N's. Their prices tend to be on average cheaper than B&N's as well.
And because I know someone is going to say "you can only buy books for the kindle on Amazon" this is not true. smashwords.com is my favorite site for getting books other than the ones on Amazon.
The NYPL library system has approximately 15,000 eBooks I can download for free to the Nook or other non-Kindle eReaders. I'm sure that will grow each year. I remember last year it was about 12,000 eBooks. Most of them are the newest bestsellers. My choice is pretty clear.
Where it says format, when you switch it to PDF, hit enter to see how many eBooks come up, it says 13,450. When you do the same for EPub, it says 1,854. You can also enter your favorite genre(s) to see how many books are in the system.
I do download free Kindle books for my Kindle for PC software. So, if there is a book I just have to have that isn't available in ePub/PDF format, I can read it on my laptop.
There are about 5 threads that have a ton of info about this same topic. Just dig around for a few minutes and you can gain a ton of valuable information.
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