Can we run both 1.1 and 2.0 web projects on the same Windows 2003 server? The answer in short is yes. IIS 6.0 can run both ASP.NET 1.1 and 2.0 web applications simultaneously on the same server, if each version specific application is assigned a different application pool. Now what is an application pool? Click the link for the complete solution: http://www.webcosmo.com/listing/Details.aspx?countryId=1&gId=1&postId=2748
All you have to do is set the version in IIS. <website name> (right click)->properties->asp.net tab->asp.net version
Setting only the version wont work. At least didn't work in my case. I ran into this situation recently. First tried changing the ASP .Net version from the website properties. Didn't work, but my other sites running on .Net 1 version stopped working. Then I tried separating the worker processes for the .Net 2 version websites creating a separate application pool for them. That worked. However if you using AJAX on .Net 2, you have to do some more work e.g. copying some extra dlls for AJAX, change the web.config to fit the scenario. So far I like .Net version 2 except the Build Website creating dynamic dll names. That holds us reusing components among projects. Thats quite a bit of change from .Net 1.
create separate application pools. put all your 1.1 sites in one pool. the others in the 2.0 pool. mixing them will cause errors! seen it 100 times.. usually when i start a new site and forget to change the asp.net version in IIS.