For me Kindle is better. Mainly because I actually like that it index's my books and if I want to search for a phrase, it doesn't just search 1 book, it will search my entire library. Its a useful feature for me because I like to look at sentence structure, so I'll often compare how different writers handle the same phrase.
I hear there are more features that Nook doesn't have but thats the main one for me. Kindle didn't have the library feature but now they have that as well, and I want a 3g option.
Oh, and prices. I avoid Agency books and I'm finding Amazon is usually cheaper with small press/ independent publishers. I do own a Nook Color, and I love that, but I think I have 1 book from B&N on it because it had a free promotion going at the time which made the book I wanted cheap.. It was free..