Assuming you got the e-reader and not the tablet, I'd say Kindle since PDFs are a big thing for you. You can root the Nook Touch pretty easily (Still trying to decide if I will rot mine or not) and get all those functions anyway, but it's native for Kindle and doesn't require voiding the warranty. Of course, you can unroot android devices and ignore the warranty problems, so that's not really an issue. With the availability of Calibre
I'd say it's mostly a matter of consumer principle which one you choose since they are both quite good at what they do.
When it comes to the tablets they have, I'm not quite as sure. They all have decent note taking tools on them now, though the tablets are a little more intuitive with it. I haven't had a chance to use the Kindle tablet yet, but if you plan to do a lot of actual book reading as well, then I'd still suggest the dedicated e-readers. From what I've seen of the Kindle Fire, it's not going to be that much different from the Nook tablet outside of giving you streaming services if you are a Prime member. The e-ink screens are just a ridiculous step up from reading text on an LCD and I can't really recommend the tablets for that.
I guess if a full browsing experience is important to you, the tablets are a good choice as they'll also give you the full color pdf and slightly better note taking capabilities, but personally I'd go the wi-fi Nook Touch/Kindle touch and download Calibre
immediately either way.
Edit: Also, keep in mind if you are seriously looking at the tablets, the Kindle Fire is almost a year newer and has a dual core processor, so it is likely going to be a bit snappier and more capable with multi media services.