First off, I didn't like Apple's Launchpad at all, but lately I am growing to love it. But I noticed that, apart from XCode only Apps located in /Applications are automatically added to Launchpad which made me wondering if there is a way manually add/remove items.
Yes. You can both clear out launchpad and put in your own stuff (by dragging to the icon). Check out the script here:
which will get you started (and finished).