Here's another little nice idea. Apologies for the shite ms-paint drawing, photoshop has decided to corrupt itself.
I doubt a new panel with a folder tree view would be that hard to put in as I believe it's one of the default window panel things.
Basically the texture browser would have a folder tree panel to the left hand side, which would allow you to manually select the contents of each wad. As well as the "root" folder, custom texture folders could be created that you can add individual textures to; so you could create yourself a "nature" folder that contained your own favorite grass / tree / rock textures, and "triggers" or "floors" or "weird computer shizznizz" and so on.