I develop with 1.1 and 2.0 - When VS 2003 creates a web solution it is configured to use the 2.0 runtime. Placeing the following code to the Global.asax’s of your 1.1 projects and setting execute permissions on the aspnet_regiis.exe helps much.

protected void Application_Start(Object sender, EventArgs e){
  if(System.Environment.Version.Major == 2) {
    System.Diagnostics.Process p = new System.Diagnostics.Process();
    p.StartInfo.FileName = "%WINDIR%\\Microsoft.NET\\Framework\\v1.1.4322\\aspnet_regiis.exe";
    p.StartInfo.Arguments = "-s W3SVC/1/ROOT" + Request.ApplicationPath;
    p.StartInfo.UseShellExecute = false;
    p.StartInfo.RedirectStandardOutput = true;
    p.Start();
  }
}