Avenarius,
How good or bad a PDFs document displays depends on how they were made, instead of the software which you use to read those. Why? because the format itself. PDF was designed to display documents (not books) in the exact way they were created, "as is".
Right now, they are two good devices for reading PDFs: iPads and Kindle DX (because the size) But to be fair, just iPads can provide an "ok" experience and that's because third party applications, not just the iPad itself.
On my Galaxy Tab I use ThinkFree and is not too bad.
Sony devices are also good but the small screen size (compared to Kindle DX) is annoying; they do have great annotations and zoom capabilities though, not bad for an eink device.
Sorry for being honest but I think that you did not do your homework before buying the Nook Color.
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