One way to do that with MobileMe/.Mac is to use advice from a Macworld article back in March to put emails in either Action, Filed or Later. That way it keeps your inbox empty or at least manageable. Here's the article:
http://www.macworld.com/article/1395...our_inbox.html
These days, you don't need a million folders, especially with Spotlight search. Just type in what you're looking for.