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Case 1: After the client changed the Application pool in Windows 2003 IIS 6; their web site showed this error "Service Unavailable"

Case 2: The IIS server receive Event ID 1039 - The Application pool 'application name' is being automatically disabled due to a series of failures. The process id was 2472, 3000, 1096, 2800, or 2980. The data field contains the error number.

Case 3: Application pool stops running.

Resolution: enable "Run WWW Service in IIS 5.0 Isolation Mode". To do that, open the IIS Manager, right click Web Sites and select properties: Select the Service Tab. Check "Run WWW Service in IIS 5.0 Isolation Mode". Restart of IIS.

Note: You can run IIS 6.0 in one of two modes: worker process isolation mode or IIS 5.0 isolation mode. Worker process isolation mode is the default mode, that is, the mode that the server runs in on a clean installation. You can use IIS 5.0 isolation mode to run applications developed for older versions of IIS that are determined to be incompatible with worker process isolation mode.

Also check these MS articles:

You receive a "Service Unavailable" error message when you browse an IIS 6.0 Web page on a Windows Server 2003-based domain controller
http://support.microsoft.com/kb/842493

You Receive a "Service Unavailable" Error Message When You Browse a Windows SharePoint Services Web Site
http://support.microsoft.com/kb/823552

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