I use Axure, and one of the brilliant guys on this list suggested I add the
functionality of Protonotes to allow commenting, which my company also
wants. The downside of Protonotes is that it is essentially a bit of code
you add to the header of each html document Axure spits out when you
generate the prototype.
However, another brilliant person wrote a little applet that you insert into
the folder in which your generated prototype resides, then run the applet,
insert your Protonotes code into that, and it automates the adding of the
code to each html document.