Here is an interesting variation on the DevNotes theme, in which the Notes and the Prototype are displayed in completely separate browser windows. The Notes continually window monitors the Prototype window and keeps the two in synch.

This may be a solution to the problem of annotating a frames-based prototype.

Please be warned, though, that this application is still in a very early alpha stage, and should be used with appropriate caution.

I look forward to any comments.

Thanks very much,
LeeBB