For some reason I didn't feel comfortable working with web site in VS 2005. May be I was so used to working with project type web application in 2003. So I decided to convert few of my existing 2.0 web sites to web application projects.
Scott Gu posted a great reference in converting one. I hit a few bumps with my profiles, other than that it was a smooth process. There are few known issues with the web project but if you are like me who enjoys just copying the dll for deployment
take a look.