Hmm...
If you need browsing, let's take eink readers out of the equation, because they are not for that. Plus only one that gives a basic ability for that is old Kindle keyboard I think.
Now, between stock Nook Tablet and Amazon Kindle, I personally prefer the Kindle Fire. Without rooting, you can download Dolphin browser and if you're an Android user, you know is an excellent browser. Navigation is ok on new Nook Tablet but if you want to install something (at least when I had mine) it was harder than Kindle Fire. The Fire is more open on that regard.
Now, please do not expect full Android experience on any of those devices, stock. They UI have been locked so you basically live and move inside each environment, which for Amazon is their own market and B&N their own B&N market. However, Nook Tablet has faster and better hardware. You can notice that if you watch streaming, but I don't think that's important for you based on your initial post.
Go Fire, these is why
-No need to root to get a functional device
-If you are Prime member or Amazon customer, works like a charm (talking by experience)
-Good value
-Better prices and titles
Go for Nook Tablet (no rooted) if ..
-You're a long time B&N customer
-You visit their stores frequently (in-store reading experience with tablet)
-Want better screen and speed for streaming
-One of those users who like additional space via micro SD card, etc
No matter what, please don't root any of those
... you will be a slave of future upgrades with the continuous fear of a new firmware ready to break your tablet.
In terms of PDF, no 7" tablet is good enough for that, not in my humble opinion. PDFs require a bigger screen, and for annotations a nice application that can handle that too. iPads are great for PDF reading. If you are not planning to edit any PDF document, Nook or Fire may or may not work for you. Nook Color does not remember last page while reading PDFs though (or was like that a year ago when I bought it) I have not tested PDFs on my Fire yet.
EDIT: ops, I noticed you said Nook Color, no Nook Tablet. If you're referring to old Nook Color device, go Kindle Fire, no doubt about it. Fire is less heavy and better device, in my opinion. If you are looking for a reading device I believe Fire is more comfortable and better on that.