I have a script that monitors my desktop. Any file not modified within the past 8 hours is moved to a folder dated for the end of this week. That gives me 52 folders a year, granular enough to find a file manually if I know roughly when I dealt with it.
My desktop stays clean except for what I'm actively working on, and I don't look for files hierarchically or by category/tag. To find something, I use Spotlight search. That's faster than navigating a folder hierarchy would be even if I knew exactly where the file was.
That's also why I love Gabor's reMail on the iPhone.
I am having trouble understanding what the problem is, here. I also suspect this may be a Gmail problem rather than a tagging problem.
I frequently put different emails from the same conversation in different folders, because they contain different types of information that I need to do different things with.
GMail will not let you do that.
You need to be able to specify both parent and child tags to be able to facilitate search and give users something that isn't too confusing re: organization.