FWIW, I do like how 3D Coat has hierarchies, instancing and grouping. Michael, you might want to take a peak if you haven't.

Basically, they use "Layers" (as in Pshop) with the standard layer controls (delete, duplicate, new) at the bottom of the palette. You can drag layers around to form hierarchies. Each layer as a 'settable' origin as in translation and rotation zero-sets. This way you can rotate and move wherever you want and still bring it back to zero.