I, too, have brought this up before. Panes are used as a sort of graphical quick-search. And as you've pointed out, making them hierarchical only works for hierarchical relationships (hey, imagine that!). For non-hierarchical relationships between fields, we need something else.
I think an intelligent AND/OR search is the way to go. For example, Adobe Photoshop Album does something like this:
http://pages.sbcglobal.net/scottraymond/AND-OR.jpgMatching is "AND", Closely Matching is "OR", and Not Matching is "NOR". This way, you can quickly select one ore more fields (and one or more items in a field, for that matter), and then see what the results are. If there are any AND matches, it defaults to AND (i.e. Matching). If there are only OR, it defaults to OR (i.e. Closely Matching). And if there are only NOR matches, it should probably default to OR and have no matches.
This is a really great way to use the panes to search for photos.
Any agreement?
Scott-