I thought this was an interesting comparison between the Nook and the Kindle. The one thing the video didn't address, and the deciding factor for me, is that the Nook offers much more format flexibility. Owning a Kindle makes it nearly impossible to switch to another ebook reader, because the format is only readable on their own device (or on computer and iPhone apps, but Apple may eliminate those from the app store, and who wants to read on the computer?). Plus, the Kindle doesn't allow you to purchase ebooks from other sellers and sideload them onto the device — which eliminates library ebooks as an option. Since my library has a great selection, and I get a ton of free ebooks from Barnes & Noble and other sources, the Nook was the obvious choice.
For a more detailed analysis of the Nook's benefits and flaws, check out this review of the Nook.