Apple - How to remove an empty group in Launchpad
Previous answer didn't help me on Yosemite - when I dragged app into the empty folder the app just disappeared for a while and the folder was still there, empty and disturbing. But then I've found a way to fix it without resetting Launchpad:
Click and hold any random app until all icons start shaking, then drag the app on the folder, DON'T RELEASE, and drag back into its place. Right after dragging back the empty folder has disappeared.
If you move an app into the empty folder and then go into that empty folder and drag the app back out onto the launchpad the empty folder will disappear.