I'm not familiar with it, but doesn't AppleScript let you do things like this? Might be worth checking out.
Why not make a script that opens the application for you (and handles the Time Machine stuff)? You could give it the normal icon and all that, I'm sure. This might result in upgrade problems though -- I have no idea how OS X handles package management.
And why not a daemon? You could use cron, which is a daemon, to check every minute to see if you are running one of the applications, and if so, call a script to do the Time Machine stuff. Despite running every minute, it's actually very low overhead. If you really need it to handle this in less than a minute after startup, you could make the script check for the application, sleep 30 seconds or so, and then try again.