When reviewing and editing papers, my advisor likes to use his copy of Adobe Acrobat to mark-up the insertions, deletions, and add comments to the original PDF. This works nicely, but when overlapping comments are present, such as a block comment over an entire paragraph with sentence-specific edits “underneath” the block comment, none of the “standard” PDF viewers on Linux (including the official Adobe Reader for Linux) are able to access the buried mark-up. Fortunately, I have discovered that a freeware program called PDF XChange Viewer can be easily run using WINE, and allows you to view, edit, and create PDF annotations. I haven’t tried creating or editing annotations, but I certainly do use it to delete block annotations covering up the more specific edits.

via Finally, real PDF annotating under Linux! (with help from Wine)