In May Microsoft released Service Pack 3 for Microsoft ISA Server 2004, when I attempted to install this update it would bring the firewall down and the service could not be restated.  It would result in leaving mixed components on the ISA Server, causing the service startup to fail.  I have now managed to apply this service pack without issue.  Below is the method that I used:

• Download Service Pack 3 from the Microsoft ISA Download Site for your ISA 2004 edition
• Disable caching, it can be re-enabled once the update it complete
• Make sure all ISA UI are closed and no other ISA utilities are in use
• Install SP3 using this command line:
  • Msiexec /p <FullPathToSP3Package> REINSTALL=all REINSTALLMODE=omus SKIP_DIAGLOGACLS=1 /l*v C:\ISAsp3.log

If this still fails, re-apply SP2 to get get the ISA service operational again.