ESRI is changing the way the ArcGIS Server works in ArcGIS 10.1, See Considerations for ArcGIS Server developers: A look toward 10.1
We build a lot of SOA webservices leveraging the ArcGIS Server. These are mostly built using the pattern shown here: How to create a geocode and search Web service one of the reasons for building our web services using this pattern, was that the support for Server Object Extensions were poor and still is in ArcGIS 10. You needed to create COM enabled classes that has to be registered on the server etc, no tools, you need to write own tool (Or download SOExplorer) see: SOE Web services
To make the transition easier, I think that ESRI need to give us better tools to handle the SOE, SOAP and REST in ArcGIS Server and in ArcGIS Desktop/Engine. Also provide a solid pattern on how to build enterprise systems where the GIS systems can communicate with other business systems.