Jarnal - is tool that can be used annotate PDF documents. It is java based. It also has support for collaboration. One person can start it in server mode and another can connect.
One thing that it is useful is to highlight text in a PDF. You can also add small notes to the margin. If would have been good if there was an option to hyperlink some portion and add annotation as a tool tip.
It does allow you to do a lot more stuff, but pretty difficult to use with a mouse. Maybe it would be more useful with a tablet.