Answer
The recommended order of installation when installing ArcGIS Desktop, ArcGIS Server and Business Analyst Desktop and Server 9.3.1 on the same machine is as follows:
1. ArcGIS Desktop (ArcEditor) 9.3
2. ArcGIS Server (.NET) 9.3
3. Business Analyst Desktop 9.3
4. Business Analyst Server 9.3
If upgrading to a newer version, install the upgrade in the above order.
When uninstalling, remove each product in the reverse order.