I have a rooted nook, actually I'm running nookie(Android 2.2) on my nook and think it is a great platform for reading PDF. It's small enough to carry and power enough to read any scan based PDF.
That said the samsung tab has more memory, a faster CPU. The experience on the tab will be quite nice.
My wife has an iPad and it is very large. It makes it easy to read larger PDF, since you most likely do not have to zoom or refelow the PDF. But the size and weight do make it awkward to port around vs the 7" screens which are small enough to slip in any pocket.
For the software I strongly recommend RepliGo it is by far the best PDF reader on the android market. ezPDF is also nice but it is not as fast and does not have as many features.
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