So, in light of the comment/chat we had under your question, using phpseclib, you should be able to connect to the remote machine, which will run your the application:
require_once('Net/SSH2.php');
$ssh = new Net_SSH2('winhostaddress');
//if needed:
if (!$ssh->login('user', 'pass'))
{
exit('Failed to connect to win');
}
$ssh->exec('C:\\Path\\to\\app.exe argument1 argument2 argument3');
That should do the trick. When using flags, like on *NIX systems: ls -a, you should know that the Windows counterpart is /. Other than that, it's all pretty much the same. escapeshellarg is not to be forgotten, when passing client-data to the executable.
Arguments containing spaces should be delimited using double quotes.
If you're not sure weather or not the application you're launching is accessible to the user you used to connect via ssh, try prepending this to your actual command:
runas /user:username C:\\Path\\To\\App.exe
Where username is a user of which you're sure that has the appropriate privileges. Note that you might be prompted for a pwd.
For any other issues, here's some related questions: