The keyboard input queue records all the unprocessed keypresses that your user has typed into your game. You can read these keypresses one at a time using the Keyboard Raw Key command, after which they will be removed from the queue.
Calling 'Clear Keyboard' will discard all the keys that haven't yet been read from the queue. This is a useful thing to do before inputting a string from the user, eg before they enter their name into the high score table. This is because the keyboard input queue will likely still contain many keypresses from when the user was playing the game, keypresses that you don't want to be typed into the highscore table as soon as you start reading it.
(For information on easily inputting strings from the user, see the String Editor suite of commands).
Clearing the keyboard input queue is functionally equivalent to calling Keyboard Raw Key until it returns 0.