As far as I can tell, to be able to annotate PDF documents you have two choices:
A) Each user can purchase a full copy of Acrobat, which provides tools like Highlight and Note (so you can highlight text then attach a sticky note to it, which is saved within the PDF file).
B) You can purchase Document Server for Reader, for $75,000. This runs on a central server and enables the annotation tools in Acrobat Reader, so all users on the network can add comments to PDF files.
For both these options, Allow Comments must be enabled when creating the PDF file to be annotated.