I like marking up PDFs as well (in my case, using an old Windows XP tablet), so I was curious about what this iPad software does. And good news, it appears that annotations
are preserved in the file itself. According to
this page on the Goodreader website (http://www.goodiware.com/gr-man-view-pdf.html#annots):
Quote:
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All annotations that you create or edit in GoodReader - notes, highlights, markups, and drawings - are saved in a PDF file, so you will be able to see them later on a computer or in another copy of GoodReader on your colleague's device.
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This means your annotations should show up whenever you open your file, on whatever computer you use.