Attendees on an Axure course last year were raving about Protonotes but I've only just got around to investigating.
If you are creating electronic prototypes with HTML or a prototyping tool like Axure, Protonotes allows contributors to add comments via sticky yellow post-its to your design. Looks like a really easy and useful way to collaborate in the prototying process. Quick and easy to set up and best of all, it's free.
Protonotes try out page