Hm... I've been quite happy using an Open Source tool called FreeMind. It seems to be a "tree editor", although I'm not sure it quite satisfies what this author is looking for.
Are any of them scriptable to the point where we could add our own desired functionality? Python preferred for me, but I'd learn another language if the app was compelling.
Screenshot: http://freemind.sourceforge.net/wiki/index.php/File:FreeMind...
Website: http://freemind.sourceforge.net/wiki/index.php/Main_Page