Manually removing a parked domain is indeed a tough job. This article should help to make your job a bit easier. I would strongly recommend you to keep a backup before you edit the files.
Grep the /var/cpanel/users folders for the domain that you are looking for and remove it from the user file in question
(this will also tell you who owns the domain).
Remove the domain entry from /etc/named.conf and the cooresponding .db file from /var/named and restart your bind server.
Remove the virtual host or ServerAlias (whichever is applicable) from the /etc/httpd/conf/httpd.conf file and restart Apache
Remove files with that domain name as the filename from /etc/valiases, /etc/vdomainaliases, and /etc/vfilters.
If the domain is in /etc/localdomains or /etc/remotedomains then remove it from those files as well. Same goes for /etc/userdomains.
This should pretty much wipe out the domain and you can re-add it whatever account you wish if that is want you want to do or just leave it gone!