Are there any full featured pdf readers that integrate comment function?
[lib]poppler recently gained support for the annotations defined in the newer Adobe PDF specifications, and this has been implemented in evince. Unfortunately, it still lacks some features, such as the ability to delete annotations (IIRC, this is due to lack of support from poppler, not evince), and I had some issues regarding editing already existing comments (but I didn't have time to debug these properly).
So, on one hand, evince has, through poppler, support for standard, built-in PDF annotations, OTOH said support is not (yet) perfect.
This should also mean that other tools using poppler may get this kind of feature in the near future.
One thing you may find annoying is the lack of a "save" feature. It drives me mad, having to use "Save as" each time I want to save a copy of the annotations (I used windows (non-NT) some years ago, so I still have, once in a while, this strong urge to save my work frequently) — but, anyway, evince is intended as a viewer, not an editor, so enforcing "Save as" is really the way to fit this into their UI metaphor.
About portability, depending on where you go, maybe it suffices if the tool lets you grab the "annotation layer". I remember walking through a layered annotation tool for postscript many years ago (and at that time it was already old code, which would need some work to build) — if I get the time and I find myself needing PDF/postscript annotation tools again, I may go looking after that so that I can hack it...
Since Version 0.17, Okular supports annotations saved to the PDF file. For this to work, you need to have a Okular compiled against a recent version of libpoppler (0.20+, this should be the case in any up to date linux distribution), and you need to use the "Save as..." command - otherwise the annotations are just saved to Okular's config directory, and only accessible by Okular itself.
This is proper PDF annotation, and can be edited by other PDF annotators, and extracted by other tools. For example, the annotations can be extracted to notes in Zotero using ZotFile.
Okular currently supports saving the following annotation types to PDF:
- Pop-up notes
- Inline notes
- Text highlighting
- Text underlining
- Freehand lines
- Polygons
- Ellipses
- Rectangles
Each type of annotation can have a text note attached. This appears to be most of the annotation types supported by the PDF specification.
Okular also supports "Stamp" annotations (adding an image), and these annotations do not save correctly to the PDF - the image does not appear, but any text annotation does get saved, as a kind of hidden pop-up note.
This might not be the satisfying answer you are looking for, but PDF-XChange reader has never given me any qualms under WINE and it is by far the most powerful third-party PDF Editor out there (almost reaches feature parity with Adobe Acrobat Pro).