I really love using folders on my imap account. This is ( I think ) one of the main reasons why I don't use gmail, labels are just not as good as folders.
I have tens of folders and message filters for each folder, I'm subscribed to various email lists from the freebsd project, Linux kernel, gentoo, postfix, qmail and some others and I use thunderbird with filters to put messages from each list in it's own folder. When you go in thunderbird to set a new filter and you want to move messages that match a certain criteria in some folder, you get a list of all folders in all thunderbird accounts. This is really a pain if you have more then one email account set up and in each account you have 20-30 or more folders.
My folders are well structured so I have just a few top level folders and then each has subfolders. In thunderbird 1.0.x you would get a list of top level folders that you could expand or colapse as you wanted, that was great but now in 1.5 when you
want to find a folder you see the whole list of folders in all accounts with every folder expanded and you can't colapse them. This is really annoing. I wonder why they changed the original behavior.