The black flag with skull and crossbones is universally understood as a sign of pirates. But there were a wide variety of different flags flown by pirates to engender fear in their opponents. Many pirates simply flew an unadorned black flag, or a red one, to indicate that they were outlaws, not bound to the rules of engagement, and that they would torture and kill everyone on board unless an immediate surrender was tendered. Pirates would also keep a number of flags of various nations on hand, to fool other ships into thinking they were friendly. When they got close, the black flag would come up, and often the victim ship's hands would jump overboard in terror. If the ship refused to surrender, a red flag would mean the ship would be taken mercilessly, and all hands killed.
In the early eighteenth century, the skull and crossbones motif became popular among pirates. The flags were handmade, and many different variations existed.
The Jolly Roger of Edward England
Calico Jack Rackham
Some pirates used a different device entirely, such as an hourglass with wings to indicate "time is running out," or the Devil stabbing a heart.
Edward "Blackbeard" Teach
Black Bart Roberts
This only serves to indicate the endless ingenuity and creative expression that pirates of the Golden Age represent!