One big runtime on extrenal drive:

Character
 - Clothing
 - People
 - Animals
 - Other Figures

Hair

Poses
 - People
 - Animals
 - Other Figures

Props
 - Buildings and Structures
 - Weapons
 - Domes, Spheres, etc
 - Outdoors
 - Other
 - etc...

Of course, subdirs under those.  (i.e. people has Daz/Poser/other...then under daz, a3/v4/m4/etc) 

The rest of my runtime is a mess

When I download, I put into a fake runtime, then move from there to the right spot in real runtime.