so some applications that are installed the ownership and group are "nobody" this means that I can't simply uninstall and delete the app. 

I can't even open my FTP and delete the app because it gives me permissions error.

The only way i know is to SSH into the server to do a sudo RM command of the offending files. - Fortunately I have a dedicated server with root access - however I imagine this may not be the case for other hosting deployments.

What hex must be done so that any directory file created / uncompress installed / inherits the sites ownership permissions?

 

'nobody' is the user associated with Apache as standard, this is completely normal behaviour.