Dear Users,
Please find the below links and try your own way to take the backup. We are suggesting to take the scheduled database backup, which will take care of your applications and workspaces.
http://iadvise.blogspot.in/2006/11/automatically-backing-up-your-apex.html
http://jes.blogs.shellprompt.net/2006/12/12/backing-up-your-applications/
http://www.grassroots-oracle.com/2010/02/automating-apex-backups-from-db.html