Since answering this question, I have come to understand that there is a distinct difference between pdf editing and pdf annotation. Proper annotation is done using a non-intrusive/non-destructive pdf annotation markup language that can be changed, rearranged & cleaned-up/deleted. So while xournal and inkscape allow "annotation", it is not in this language and it is not necessarily non-destructive. Meaning, those using other software may not be able to read it, or can only read the part that ended up permanently changing the document. The only proper annotation software available on linux, that is software using the pdf annotation markup, is the DocuTrak software (below) running under wine. (As of 2015.)
As answered previously:
I can't help you with Master PDF Editor, but I have used DocuTrak's PDF Xchange Viewer, which allows document annotation. It's free (as in beer) and it seems they now also have an "Xchange Editor" (which I have not explored - perhaps they've just split out the editing functions?):
It's a Windows product, but the Viewer, at least, is a stand-alone exe and runs under wine (the MS Win Compatibility Layer). You can find reports on wine software compatibility at winehq.org. See, eg.:
Just install the package "wine" and then follow instructions from there. I remember it as being quite straightforward.
The only other software I've tried for pdf editing (not just annotation) on ubuntu is the pdfedit package, but that's real alpha software.