Hello.
This is how I would do this. It is fairly simple and works well.
First you need to write a console app or what ever to register an application to a URI scheme. This can be part of your installation program (I guess this is what WebRunApp does).
For example this is how you would register notepad:
var key = Registry.ClassesRoot.CreateSubKey("customProtocol", RegistryKeyPermissionCheck.ReadWriteSubTree);
key.SetValue(string.Empty, "URL:customProtocol Protocol");
key.SetValue("URL Protocol", string.Empty);
key = key.CreateSubKey(@"shell\open\command");
string exe = @"c:\windows\system32\notepad.exe";
key.SetValue(string.Empty, exe + " " + "%1");
Once this is done you can use that in a webpage, here is an example firing up notepad and your email client:
<!DOCTYPE html>
<html>
<body>
<a href="mailto:">Click here to mail</a>
<br/>
<a href="customProtocol:">Click here for notepad</a>
</body>
</html>
It's that simple. Enjoy :)
Valery.