While Typing I Realised It Would Be A Terrible Feature Request So Here
Re:
https://twitter.com/kristianduske/status/508004011023540225 "TrenchBroom 2 now has a layer system. Layers can be hidden and locked individually."
Please add some more options:
"Exclude from compile"
"Hide all layers but this one"
Being able to group layers into (multi-level) groups would be great.
Also being able to assign colors to layers/groups.
Can you duplicate layers?
Can you drag'n'drop prefabs from the TB Store into the list????
Maybe check out how QuArK does things, random link to its documentation where you can see some of the GUI and features:
http://quark.sourceforge.net/infobase/maped.tutorial.advanced.html#grouptechniques