You are in luck: you can already do this with AppMenuBoy. If you put
aliases in /Applications, AppMenuBoy will follow them.
I keep most of my applications in a "3rd Party Apps" folder, but the
developer tools install into /Developer/Applications. A simple alias
from there to /Applications, and AppMenuBoy shows them too.
AppMenuBoy builds its menus when it starts. If you edit the
application folder tree, you'll need to restart AppMenuBoy to see the
changes.
All of the above is assuming that a single hierarchical menu is good
enough. If you want multiple icons in the Dock, you'll have to do a
bit of programming.
You can have as many AppMenuBoys as you want, if you are willing to
fetch the source code and compile it. You can set which folder the
program looks at, and what the application's icon is. If you edit the
application's signature in its Info.plist file, you can easily have
multiple copies running simultaneously.
Or, have I misunderstood you completely?
-- David Phillip Oster