Unfortunately, the Folderpane Tools-plugin I used for rearranging my accounts in Thunderbird isn’t TB3 compatible (yet?!). Although it claims to work with all Thunderbird versions starting from 1.0 it just throws out parsing errors with the current Tunderbird beta.

But the plugin doesn’t do any magic tricks, of course. It simply reorders the accounts in the corresponding preferences file prefs.js. Open the file (usually located in with ~/.thunderbird/[profileName]/prefs.js) with your favourite editor and look for a line like

user_pref("mail.accountmanager.accounts", "account1,account2...

Rearrange the accounts manually and your done.

Note: You may want to close Thunderbird and make a backup of the file before editing it. Just in case…

Resources:
https://addons.mozilla.org/en-US/thunderbird/addon/258
http://advancingsf.blogspot.com/2006/11/reorder-accounts-in-thunderbird.html