[fjtorres]

Interesting quandary because, frankly, the overlap between the two isn't that big.

NookColor is (mostly) about color ebooks for kids and magazines, Kindle is (mostly) about novels and recreational reading.

Kindle is about free 3G and extreme battery life; NookColor sacrifices both to provide color and a responsive touch screen.

Both will do magazines but if magazines are the bulk of your reading you want the NookColor most likely because of the color.

If color *isn't* that important then likely a Kindle will do.

But if PDFs are job one, neither is exactly great at it; depending on the file they will run from tolerable to good enough but nothing smaller than 9inches is going to be great at PDF.

What I would suggest, however, is that you might want to broaden your search.
If cost is an issue, an Android Webpad like a Pocketbook IQ or Velocity Micro T301 would give you the equivalent of a Color Kindle with the ability to also handle epubs and PDfs. Some can run Nook, too. All can run the Overdrive Media Console to access library ebooks and Adobe's own reader app.

A Kindle DX would give you a big enough screen to properly display PDFs plus all the other Kindle pluses. And if PDF matters more than magazines...

Or, if the budget allows for an iPad you could install both the Kindle and B&N apps and get a mix of all the desirable features.