Deploying asp.net web application in a new server like w2k3, ensure following steps incase if you see HTTP Error 404 – File or directory not found error …
1. Allow asp.net v2.0.50727 under Web Service Extensions section in IIS
2. Run aspnet_regiis -i @ command prompt from the respective (32-bit/64-bit) frameworks directory
3. Set proper asp.net version at the virtual directory level