I just discovered, if you 'Control-Click' on an application in the dock while it is starting up, you can then select Force Quit and kill the application before it completes the startup (even works with the Classic icon). Not sure how clean this is, but it gets the job done.
[Sudo Editor's Note: Force quitting an application during start may cause file corruption and damage to your application, or worse, your system. You should avoid this method whenever possible. As a side note, I am pretty sure that it was 'Option-Command-Esc' that killed an application during startup, and not Command-Period. Since I do not have OS 9 running now, I was unable to verify this.]

