f.e. Amidock crashes at boot:
Program Failed (errpr #80000004)
Wait for disk activity to finish.
Suspend - Reboot
I also get this on other tools like format. Others just refuse to start at all, like HDToolBox.
Sometimes it means your install misses something in Classes:Gadgets. Make a comparison between your install and the OS 3.9 CD. I did have that problem.