1) find the launchpad sqlite3 db. This is under the com.apple.dock.launchpad buried in a subdirectory in the /private/var/folder.
In most cases since this was one of the first folders created; it should be in the first folder and first subdirectory of that folder/folder. cd into the first folder after a ls.
In my case it was here: /private/var/folders/mb/br6t4l8d5svbdx8w4r966y1w0000gn/0
localhost:0 dc$ ls
cd into com.apple.dock.launchpad folder and verify there is a db folder. The sqlite3 database is under this directory in file db. Run sqllite with the path to this file if you aren't in this directory. localhost:db
dc$ sqlite3 db
SQLite version 188.8.131.52 2014-03-11 15:27:36
Enter ".help" for usage hints.
List the app names
sqlite> select Title from apps;
Calendar... (rest deleted)
Delete the app title
>DELETE from app where Title="YouTube";
cntl-D to exit
killall Dock to reset Launchpad; verify gone
Look in /Library, etc.. to clean up application created files.