I must confess, this has haunted me for months before I could find the solution. I went from ICS to JB and had the same problem. Off course my phone is on the Stock ROM.
The following steps needs to be taken to clear this out.
1. Reboot the Phone – Duh!, I guess you guys would have done this.
2. If you have voice mail services On, please ensure you have listened to all your Voicemails, and if possible deleted them and then rebooted your phone
If the above 2 steps have not cleared it out, here is what you got to do.
Go to your Settings app and click on Application manager, Scroll to the right , to select “ALL” and then select “Badge Provider”. Click on Clear data
If needed, click on Clear Cache also (In the badge provider) and then reboot the phone. Voila! … The notification should now be gone.
Hope this helps !!!