One of the big hassles in my job has been attempting to organize NDA agreements with customers and partners. The fun and games begin with multi-party NDA agreements.
The VC community has solved the problem by avoiding NDAs where ever possible, as outlined on Ask the VC and by Rick Segal on his blog.
To my mind, the act of non-disclosure is a question of trust. If you really need to rely on NDAs then the relationship between the parties should be questioned. Maybe it is more like patents, you file them in the hope you never have to use them … but just in case.
Bonus Link: Brad has an article from last year on NDA’s too.