My OmniGraffle stencils menu was getting a bit chaotic. One big long list. The default Omnigraffle stencils use sub-menus. For instance the business stencil sub-menu.
But all the downloaded ones just wound up in the main stencil menu.
So I created some sub folders inside ~/Library/Application Support/OmniGraffle/Stencils and dropped some of my stencils there.
It just worked ™.
I tried symbolic links to have one stencil in multiple sub-menu’s, but that does not work. So I wound up copying them.
This looks a bit nicer:
Trivial.
KnobsLeversButtons 
you’ve just saved my day. smart and simple. my own chaotic stencil panel was driving me nuts! thanks