Its not a perfect or even a good solution but I made some scripts to hide/unhide subtools easier and a pseudo grouping based on keywords in the name. That's about the best you can get currently.
^ Wow. That actually makes ZBrush seem like, well, "normal" software.
It is quite brilliant. I thought I was in some sort of wonderful Zdream when I first saw it. It runs as a floater 'kind of' within ZB. Still in beta, but some great features and a bright future/fast update dev process. Free to try with a few limitations.
Replies
http://exoside.com/zscenemgr/zscenemgr-buy/