I had a similar problem with /Developer/Applications
1)
I just used the Finder to <Command><Option>-drag the /Developer/
Applications folder icon into /Applications. The next time I ran
AppMenuBoy, it followed the alias, and I had a sub-menu of my /
Developer/Applications.
or
2)
You could fetch the source code, which builds with Apple's standard,
included developer tools, and modify it to do what you want. If you go
this route, please email me your changes, because I'm curious. The
source code can be fetched from:
http://code.google.com/p/appmenuboy/source/checkout