Perhaps this review is a little premature as I've just installed the program, but so far it seems to be working well and I haven't had the issues mentioned in some of the other comments, namely that it doesn't retain the changes after restarting.
When I installed this, I chose the option to "Install for all users". Then, I selected the apps I wanted to show, I clicked "Apply" and then "Refresh" and it made the appropriate changes. I rebooted my computer, launched LaunchPad and initially it showed "Loading Applications" and then it showed it just as I had set it up, i.e. only the apps I had selected in Launchpad Control were in my LaunchPad - just as I wanted it. I will write a follow-up should I notice any glitches but so far, so good.