Recently got hit with "Another transaction by user ... is already in progress for this app and major version." during what I thought was going to be a quick update.
Thanks to John Ballinger for posting instructions.
1. Start -> Run -> cmd
cdinto your application directory. For me, this is cd /Sites/appengine_myapp
appcfg.py --no_cookies --email=YOUR_EMAIL_HERE@gmail.com --passin rollback ./
4. You should be prompted for your password.