The documentation for running the SQL Server 2008 QFE/CU installer in unattended mode is not currently available online. The instructions are included in the updated help chm contained in the packages.  Here is a quick reference on how to run the patch installer in unattended mode:

Patch all applicable instances: 

{Patch package}.exe /q /action=patch /allinstances

Patch a specific instance: 

{Patch package}.exe /q /action=patch /instancename={specify instance name to patch}

Examples: 

(1) If you would like to apply SQL Server 2008 Cumulative Update 2 (http://support.microsoft.com/kb/958186/) in unattended mode to all instances, the command line would be:

SQLServer2008-KB958186-x86.exe /q /action=patch /allinstances

(2) If you would like to apply SQL Server 2008 Cumulative Update 2 (http://support.microsoft.com/kb/958186/) to all instances showing UI progress with no user interaction, the command line would be:

SQLServer2008-KB958186-x86.exe /qs /action=patch /allinstances