The SCCM outage was resolved last week. The resolution was masked by the central certification revocation list not being used on the clients therefore leaving a broken certificate and causing SCCM clients to fail.
The certificate revocation list issue is ongoing and is being dealt with by our Server Infrastructure Team.
A workaround has been put in place to remove the offending certificate from clients via a group policy startup script.
If you find any machine not receiving applications or software updates please check the computers personal certificate store and delete the ConfigMgr client v2 certificate, as per the previous instructions, if it still exists along with any other troubleshooting.