I like folders. I like tags. I like search folders. I think having all these together and differentiated equals clutter in the user interface.
I know this might sound too bold, but I would suggest virtual folders as a unique metaphor that would embrace all those ideas in one. When every folder is virtual it can act as a real folder, it can hold tagged emails or it can hold searches. I find no need to make it look any different from an organizational (user interface, user interaction design, you name it) point of view.
Good work anyway, Once you get this software running faster (see my other post) I'll buy it!