I alos have many runtimes - 41 now :) Then when I have downloaded something it goes into the runtime where I think will suit best.
Some of my runtimes names;

Aiko3
Aiko3 costume
Buildnings
Plants
Hair
Animals
V3
V3 Cloth
Scene

So when I want to add... lets say a chair, then I know I most likely have placed it in my runtime called "Furniture"

The trick is the make runtime after Your way to work, then orginaze things so you will find them, keep things that are simular together.

OH and I allways have Explorer open, so I can look around in my folders, so I don't have to switch runtime folder soo often (sometimes hard to tell if a thing I want is a character or a prop :))

Love Jenny