Well, in a 'normal' .NET application you can use the System.Diagnostics.Process.Start method to launch an external application.
In ASP.NET (you can also use that method) however you'll probably run into two problems.
1. Access rights. It's not given that the account running the IIS (or the .NET working process) has access to launch external applications. This you can solve using impersonation.
2. Where should the application launch? In a normal situation the IIS service hasn't any desktop (screen to place a window) associated with it.

Maybe this can help you out.

- petter