My solution to disable popup blocker(or any registry setting in HKCU) on a remote machine on an IE zone, without GPO.

So basically, the C# writes a Batch file on the user's Desktop that the user must double click so it runs under their credentials, the Batch file then creates a .reg file on the desktop that it in turn runs to change the registry setting in HKCU, then it deletes the .reg and then itself. I was proud of this a few years ago when I wrote it with the 3 nested syntaxes and all. As you can see it relies on other custom methods I wrote, but what you need to do to replicate should be clear.

     public void DisablePopupBlocker(string pcname, string profile)  
     {  
       try  
       {  
         if (PcNameIsNotNullOrVoid(pcname) && !string.IsNullOrEmpty(profile))  
         {  
           pcname = CleanPCName(pcname);  
           profile = CheckForProfileDotDomain(pcname, profile);  
           //string filename = backslashes + pcname + @"\" + cshare + @"\Documents and Settings\" + profile + @"\Desktop\Disable PopUp Blocker.bat";  
           string filename = GetDesktopLocation(profile) +profile + @"\Desktop\Disable PopUp Blocker.bat";  
           if (File.Exists(filename))  
           {  
             File.Delete(filename);  
           }  
           try  
           {  
             using (StreamWriter writer = new StreamWriter(filename))  
             {  
               writer.WriteLine(@"@echo off");  
               writer.WriteLine(@"");  
               writer.WriteLine(@"echo Windows Registry Editor Version 5.00 >popup.reg");  
               writer.WriteLine(@"echo ;Pop up blocker disable >>popup.reg");  
               writer.WriteLine(@"echo [HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Internet Settings\Zones\2] >>popup.reg");  
               writer.WriteLine("echo \"1809\"=dword:00000003 >>popup.reg");  
               writer.WriteLine("echo \"2200\"=dword:00000000 >>popup.reg");  
               writer.WriteLine("echo \"1609\"=dword:00000000 >>popup.reg");  
               writer.WriteLine("echo \"2101\"=dword:00000000 >>popup.reg");  
               writer.WriteLine(@"");  
               writer.WriteLine(@"regedit.exe /s popup.reg");  
               writer.WriteLine(@"");  
               writer.WriteLine(@"del /q popup.reg");  
               writer.WriteLine(@"del %0");  
               writer.Flush();  
               writer.Close();  
               MessageBox.Show("Created Disable PopUp Blocker.bat on " + profile + "'s Desktop.");  
               writer.Dispose();  
             }  
           }  
           catch (IOException ioe)  
           {  
             MessageBox.Show(ioe.Message);  
           }  
   
         }  
       }  
       catch (Exception popupException)  
       {  
         MessageBox.Show(popupException.Message);  
       }  
     }