First read what’s new in Exchange 2007 SP3. Here is quick guide on Exchange 2007 SP3 installation. Download Exchange 2007 Service pack 3 . As a precaution backup Exchange 2007. If you are running Exchange on vSphere then take a snapshot so that you can go back to pre-SP3 stage. Exchange 2007 SP3 is un-supported in an upgrade scenario on Windows Server 2008 R2.
To take snapshot>right click on virtual machine>Click on Snapshot>Click Take a Snapshot>Type Name and uncheck snapshot memory>Click Ok.
Stop any backup services agent such as Backup Exec or CommVault running on Exchange Server
Extract E2K7SP3EN64.exe and run setup.exe follow the installation prompt.
Once finish, reboot server. Verify all exchange related services started. Check internal and external email going and coming into organisation. Check CPU and memory uses in Exchange server. There are known issue with SP3 such as cpu sparks. install updaterollup1 for Exchange 2007 SP3 after installing SP3. You are good to go now.
SP3 Known Issue: CPU sparks
Blog by Raihan Al-Beruni 