You really should not muck with your certificates unless you know what you are doing. The Go Daddy certificates are there because they are a root provider of such certificates, so any certificate signed with Go Daddy's will need them in order to successfully initiate SSL communications. Same with the Equifax and other root providers. You'll see these certs embedded in IE/Chrome/Firefox and Windows itself so that it can successfully encrypt network traffic to any sites that use those providers for SSL certificates.
If you are worried about 3rd party certificates that might have been added you can close down firefox, to to your AppData\Roaming\Mozilla\Firefox folder, find your profile folder, and delete the cert8.db file within it...