As long as the folders that you're using in the Mail program are Smart Folders, iSync can keep everything up to snuff. Open the Sync tab in the MobileMe preference pane and you can see your choices. Unfortunately, you can't tag any Mail folder for syncing, it must be a Smart Folder. That might crimp your style a bit with trying to create a complete "carbon copy" but you can get close.
What I do, if you're interested, is I have one computer that is my Mail master where I have all my different folders for filing my mail. My other computers, 10v included, are able to see the server mailboxes, able to delete, reply, all that, but my permanent repository for locally saved mail is the aforementioned master. This is much like how one would use an iPhone -- my assumption is that eventually I'm back at my primary computer to do a little sorting. Personally, I prefer manually cataloging my mail. The downside of my method is that my remote devices do not have my Mail library for reference.
I could move to a SmartMailBox setup, but the downside of that is that once an email is automatically filed it is no longer on the server (if the Mailbox is local), so I can only see new mail on my master computer -- unless it's shut down, which keeps it from filing.
Do a couple experiments and you'll see what I mean.
---------- Post added at 06:21 PM ---------- Previous post was at 06:20 PM ----------
Obviously if all your smart mailboxes are server-centric, the auto-filing isn't a problem.
---------- Post added at 06:26 PM ---------- Previous post was at 06:21 PM ----------
Just one question... why do you have "tons of various mail folders" on your Desktop. If you keep your mail folders within the Mail program, things get a lot easier. Folders can either be local or server-based. Mail basically stores the whole mail database. You can search it either within Mail or by using Spotlight.
Mini 10v, A06, 0.8.3 Final, 10.6.2. Also: MacPro, MacBookPros, MacBooks, MacMinis, AppleTV, iPhones, iPods, Airport WDS Network. All Mac since 1984.