Mendeley has a built in pdf editor/annotator (linux, mac, windows). To persist your comments to pdf make sure to select File/"Export PDF with Annotations". Mendeley also works great for its original purpose -- organizing research papers.
In Adobe Acrobat click on: Comments / Enable for Commenting and Analysis in Adobe Reader
Now you can annotate documents with Adobe Reader in Linux/Ubuntu :)
keywords: PDF annotations comments linux ubuntu highlight
> "We need to enable commenting for Acrobat Reader 8. Is there a way to batch process these files instead of using Acrobat 8 to open each file and enable them manually?"
"Using Adobe LiveCycle Reader Extensions Server - yes, there is."
"Finally sorted this one… well if you use a mac, try using the 'Watch me do' function in automator!"