I am looking for a tool which allows me to annotate PDFs in Ubuntu and share the PDFs with annotations with people who use OSX or Windows. I cannot assume that the others can or will install special software to read the annotations.
I am therefore looking for software which allows me to make annotations in PDfs which are compatible with Adobe Reader.
What good alternatives for Ubuntu exist for this?
Look for the package "xournal" in the software center or user apt-get to install it. With it you can annotate PDFs and export them as PDF again.
Besides Xournal (see m4lvin's reply), you could use PDF XChange Viewer. The free version allows for annoting PDFs, too; it runs without problems using wine.
Newer versions of Okular can save annotations directly to the PDF file.
By default, the annotations are saved in the local directory for each user. However, if you choose "File" -> "Save as..." you will be able to save your annotations in a new PDF file, so that they are visible by any other PDF viewer. (See http://okular.kde.org/faq.php#annotateandsendtofriend )
I was searching for exactly the same. For me, qpdfview works like a charm. Annotations and text highlighting is recognised in Adobe Reader (Linux version 9, Windows. iOS). Editing done on the aforementioned platforms are recognised by qpdfview as well. It allows you to delete annotations and highlighting too, and stores annotations in the PDF.
It is free, the source code can be found on launchpad. You find it in the Ubuntu Software Center and there is a ppa for a more recent version: ppa:b-eltzner/qpdfview
Pretty old post, but still valid
Here is a non-open (but free) solution :
You can download Foxit Reader, there is now a specific version for Linux and it works fine for Ubuntu
chmod 777 ./FoxitReader.enu.setup.2.4.XXX.x64.run
./FoxitReader.enu.setup.2.4.XXX.x64.run
Assuming you want to stick to free software, I would support the suggestion to use PDF XChange Viewer, and also add that Inkscape works ok for quick annotations to single page PDFs.
It would be great to see a native version of the free PDF Xchange Viewer on Linux, but it does run fairly well on wine. If you're willing to pay for a native linux app, there's PDF Studio but it isn't cheap. (LINK)