I have the nook classic, the Kindle 3, and the Kindle DXG (second generation), and can provide some comparison for you since PDFs are an interest of mine too.
First, the nook. The nook's PDF reader provides "reflow" capability which means that you can change the font size on PDFs that are not scanned images of pages. The Kindles do not provide this capability. But the nook does not provide landscape mode, zoom, or pan. Especially on such a small display, I think these features are important if you are trying to view graphics of any kind.
The nook with softroot - I did this to mine for a while and then went back to the original firmware (and then the update to v1.5). The aPDFViewer app in the softroot package provides landscape and pan/zoom, but not reflow. The pan in this PDF viewer is rough in that it jumps from one zoomed area to another without the capability of smooth scrolling. There was an experimental version that provided smooth(er) scrolling, but it was very, very slow, which is quite annoying when trying to read a document and keep the contextual flow in mind while waiting for the next screen to display.
The Kindle 3 and the Kindle DXG have somewhat different PDF capabilities. Both provide zoom/pan, and scrolling capability in very small increments. Neither provides "reflow", so you can't change the font size in a PDF. The Kindle 3 also provides the ability to control contrast (i.e. the darkness/lightness of the print itself). This can be VERY important if the PDF displays very light, making it hard to see without darkening the print.
One thing about the Kindles overall is that they are FAST compared to the nook. With the new v1.5 firmware for the nook, page turns are faster, but nothing has changed for the PDF reader.
Personally, I have grown to much prefer the reading experience on the Kindles over the nook, especially for PDFs. My interest in getting one of these things (an ereader of any kind) in the first place was for reading sheet music. The screen on both the nook and the Kindle 3 is just too small to do this well (or any PDF that has graphics in it such as charts and that sort of thing. The Kindle DXG is very nice for this sort of thing, since it is much larger.
There are other features that some people want for their PDF reader that none of these three devices provide, but for my use, the Kindle DXG is best for reading PDFs that contain graphics and that sort of thing. I think the reflow capability of the nook is more than offset by the Kindle 3's abilities to do zoom/pan/contrast/landscape, and therefore prefer it to the nook for reading even text-only PDFs.
I hope that helps,
Tony
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