Cumulative Update 3 for System Center Configuration Manager 2012 SP1 has been released http://support.microsoft.com/kb/2882125
After upgrading to System Center Configuration Manager 2012 SP1 CU3, you will be able to identify the update as shown here.
First let us take a look at the console, after the update the console reports version 5.0.7804.1400
The console reported version 5.0.7804.1300 before updating which is CU2.
The Console update is also listed in Control Panel as an Installed Update.
The site will still report version 5.00.7804.1000 after the update.
In order to check if the update has been applied we must look in the registry.
CULevel reports 3 after CU3 has been applied.
Before updating CULevel reported 2 for CU2.
This update is also visible under Installed Updates in Control Panel.
The client will report 5.00.7804.1400 after the client has been updated.
Before updating the client reported 5.00.7804.1300 for a CU2 client.
CU3 also includes this previous released update for SCEP http://support.microsoft.com/kb/2865173
Which means that scepinstall.exe file in the ConfigMgr install folder “.Program FilesConfiguration ManagerClient” will be updated to version 188.8.131.52
And finally as reported by the client.
Also take a look at this post http://larslohmann.blogspot.dk/2013/09/endpoint-protection-client-update.html regarding the SCEP update.