I know that you've long since chosen, but owning a Fujitsu Stylistic in the 4900 series, I wish I'dve had that with Microsoft OneNote or Franklin software in school.
Doubly so with the print function in OneNote 2007. Go to the PDF page you want to cite, print the page to a page in your OneNote section. (First print the title and bibliography data, or just sketch it in freehand with the stylus.) For non-printable books, I'm pretty sure you can do a screencap, crop it with whatever tool you'd like, then C/P it into OneNote (I can't remember for sure, but I think that OneNote could do the crop of your screencap if you wanted.)
Anyway, that's what I would use today if I were still in school. Sadly, I didn't get my Tablet until I was seven-plus years out of postgrad.
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