Perhaps you could convert the "long running apps" into Win32 SERVICEs. These have a lot more control, via registry keys, as to what they look like when running.
The Windows resource kid provides "srvany", which helps launch any command line app as a service.
"For every complex problem, there is a simple answer ... and it is wrong." --H.L. Mencken
Comment on Re: Setting Win32 "Image Name" of a Perl Process