See this post. This can be used to replace notepad with other program, for example.
Under the registry key
HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution Options
create a subkey with the name of the exe you want replaced.
Add a string value called Debugger.
Modify Debugger with the command you want run.
When any user tries to run any executable with the name of the subkey, Windows executes the Debugger command with path\name of the original exe and all command line parameters appended. (Did that make sense?)