Hey Drew, nice set of articles. Have something similar at work and monitor 80+ instances and that's just MSSQL. Though we only use Rep Services to display results. The .Net is what we're thinking might be really good for us.

Gary - for named instances we have the linked server as "SERVERNAME\INSTANCENAME" and then in our servers table we have the servername as that SERVERNAME\INSTANCENAME. This wroks a treat for us. On one of our development boxes has 3 2000 and 3 2005 named instances. Can get stat's for all of them. Hope this help

Nick