I decided this needed it's very own post as it is buried in another one.

I was way too eager to finally get .NET 2.0 onto my web server and missed a step and did not recognize the red flags going up trying to tell me that I missed this step.

If you are putting .NET 2.0 onto a web server already running 1.1, you need to create a separate application pool and set the app pool for .NET 1.1 apps to one of them and .NET 2.0 apps to the other one.

Most likely, if you are not creating any new 1.1 apps, you should attach the 1.1 apps to the new app pool and if you use a default app pool, let the .NET 2.0 apps own that.

Each application pool owns a different process. So I had the 1.1 and 2.0 apps running in the same process and they were really tangling with each other. I was getting Server Unavailable errors and even had a bizarre effect on a web service*.

In case you haven't dealt explicity with application pools yet, that is a separate section in IIS. You have Application Pools Websites and Web Service Extensions. You can easily create a new application pool.

Then, in the properties of each web site you want to change, the application pool option is a drop down at the bottom of the first tab (Directory).

*That was a doozy. It was a 1.1 service that returns a DataSet comprised of 8 tables. Before returning the ds, I use XCeed stream compression to compress the stream. On the client end, I decompress and then read the stream into a new dataset. Suddenly the resulting dataset had taken two columns from the first table and created new tables out of each one. Once I figured out what was happening, I had no clue how to deal with it other than remove the compression and just return the datatable. In the end, the problem disappeared when I sorted out the App Pools!!