How to Change Mailbox Order in Thunderbird

The mailbox order can easily be changed by modifying your prefs.js file. This is located in Windows Vista and 7 at "C:\Users\your_username\AppData\Roaming\Thunderbird\Profiles\mt2ews1u.default" or, in Windows XP at "C:\Documents and Settings\your_username\Application Data\Roaming\Thunderbird\Profiles\mt2ews1u.default"
Of course, it is always good practice to make a copy of your prefs.js file as prefs.bak, in case you accidentally corrupt it.

Before editing, also take note of the order of mailboxes as it stands, then close Mozilla Thunderbird. This is the nut section of the prefs.js file:

user_pref("mail.account.account1.server", "server1");
user_pref("mail.account.account2.identities", "id1");
user_pref("mail.account.account2.server", "server2");
user_pref("mail.account.account3.identities", "id2");
user_pref("mail.account.account3.server", "server3");
user_pref("mail.account.account4.identities", "id3");
user_pref("mail.account.account4.server", "server4");
user_pref("mail.account.account5.identities", "id4");
user_pref("mail.account.account5.server", "server5");
user_pref("mail.accountmanager.accounts","account1,account2,account3,account4,account5");
user_pref("mail.accountmanager.defaultaccount", "account2"); 

In my case, account2 was a school account, account 3 my old school account, account4 another school account, and account5 a Gmail account I wanted at the second position. The order is taken from the bolded line with 2 caveats: because account2 is the default account, it is on top; because account1 is the Local Folders, it is at the bottom.  With this in mind, I wanted account5 to move up to second position and  account3 last. Here is how that line changes:

user_pref("mail.accountmanager.accounts","account1,account2,account5,account4,account3");

Save prefs.js, and fire up Thunderbird. You are all set!

Note: If you are not sure which number is what account, search for "mail.server.server1.directory", replacing the number after server with what you are searching for. The directory name should be the same as the account.