From MozillaZine Knowledge Base
The Folderpane Tools extension adds the ability to change the order of accounts in the folders pane, and chose the startup folder. The authors home page has instructions on how to use it. The account you set as the default account will be listed first in the folders pane.
Manually Sort Folders
The Manually Sort Folders extension adds the ability to change the order of the folders for each account in the folders pane. It also has a tab allowing sorting the accounts. The account you set as the default account will be listed first in the folders pane.
Manually edit the "prefs.js" file
You could change the order of your accounts in the folders pane by modifying your prefs.js file as described in this thread. If you have trouble figuring out which accounts are assigned to which account numbers in prefs.js, or if you try changing the order of accounts in prefs.js but the order displayed in the folders pane is not what you expected, see this thread for further information.