Thanks for the replies. Let me clarify my points further:
1. I know that we have the option to use either 2-tier or 3-tier architecture with Geodatabase Setup. However, in ArcGIS 10.1 Desktop the "Default" connection type is the direct connection (without arcsde service credentials (sde port, sde server name,...etc). You still can use your old "application server" sde connections files and ArcGIS 10.1 Desktop will accept them (right click on the connection properties and a new option in the type of connections will be displayed).
The Question is: what's the point of 3-tier architecture (if you upgrade to 10.1), since all connections Hits are going directly to the database SDE System Tables ?!!
The SDE Geodatabases AP are receiving either (Desktop Connections) or Map Services. if Desktop users have upgraded to 10.1 and your map services MXD's are using 10.1 connection files then there is no need for ArcSDE Engine anymore.
Remark: i am working in big corporation and we always upgrade to latest ESRI releases.
2. Concerning shutting down connections, i know that you can do that in 10.1 using the new geodatabase administration tool (this is process killing not shutting down). but how can i totally block connections to the geodatabse ?? (by the way map-services usually try to re-establish connections after killing it).
3. i don't see any clear documentation in ESRI regarding geodatabase logs in 2-tier setup for ArcGIS 10.1 , what you have provided is for 9.2 release. they should mention it in their documentation in 10.1 !!
Regards,