I've found that the empty dotfile .disabled was created in my /Library/StartupItems/Privoxy directory when I accidentally told some security checking program that I didn't want Privoxy to be started automatically. The symptom was something like the following line appearing in the /var/log/system.log file:
SystemStarter[47]: Skipping disabled StartupItem:
/Library/StartupItems/Privoxy
After I removed (with root privileges) the .disabled file, SystemStarter was able to start Privoxy. There is no mention of this behavior in the man page, nor did I see anything useful in SystemStarter's verbose output, nor the debug output that hinted at the .disabled file. And I didn't happen to see that file in the directory before, because dotfiles are not normally displayed for me.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20061204120027876