Actually, Notepad won't open either way. On a Windows system, Apache will execute the command prompt with whatever parameter you specify, i.e. cmd.exe /c notepad.
This process (as well as Notepad.exe) is a "child" process of the Apache service and is thus launched with the same privileges. The default privileges for the Apache service is SYSTEM privileges, and is not allowed to interact with the desktop itself. As such, Notepad does actually run... you just can't see it.
You can change this by altering the permissions on the Apache service. Open up the Services MMC snap-in (Start -> Control Panel -> Services), go to the properties of the Apache service, and on the "Log On" tab, place a check in the box next to "Allow service to interact with the desktop".
EDIT: Note, this change does not take effect immediately - you'll need to stop and start the Apache service so that it is executed with the new permissions.