Change account ordering in Thunderbird

To change the order of Thunderbird email accounts in the left panel proceed as follows:

1 - Open Thunderbird. Make note of current ordering of accounts. Close Thunderbird.

2 - Explore C:\Documents and Settings\%USERNAME%\Application Data\Thunderbird\Profiles\
(%USERNAME% will be automatically replaced by the current user's name by Windows Explorer)

3 - Edit prefs.js, find the following line:
user_pref("mail.accountmanager.accounts", "account1,account2,account3");
The comma separated list dictactes the account order.
Change the order to your liking.

4 - Restart Thunderbird and check results.

Source: Lego's Land blog post