The skull and crossbones originated with pirates, but its use has not always been accurately depicted in popular culture.

Pirates in the Carribean, where the Hollywood tropes originated, flew a variety of flags. They would often fly a national flag identical to, or of a nation friendly to, their intended victims while approaching them. The deception would continue until it was too late for the prey to escape, at which point the pirate flag would be raised (often accompanied by a warning shot).

The piratic insignia were used as an intimidation tactic. The message a pirate flag sent was that failure to surrender could carry lethal consequences. If a merchant ship could be convinced to give up its cargo and other valuables without a fight, so much the better.

From the victims' point of view, it was important to know if an attacker was a pirate vessel, as opposed to a privateer (a private vessel operating under a government licence to attack the ships of a particular opposing nation) or a military ship such as the Spanish coast guard. The latter two were constrained by law against killing the crew of victim ships unless they resisted, while pirates operated according to any or no rules, as they preferred.

Privateers were required to fly special versions of the national flag of their sponsoring country, while early pirates had individual insignias that varied widely. Some were green or red (French pirates in particular favored red flags to symbolize danger or bloodshed if surrender was not forthcoming). Quite often, a pirate flag was simply plain black, as flown by such noted pirates as Richard Worley, Charles Vane and Peter Easton. Edward Teach (Blackbeard) originally used a plain black flag before adopting one with a skeleton and bleeding heart motif.

What people think of a standard pirate flag design, consisting of a skull and crossed bones, may have originated with Barbary pirates or Muslim corsairs. Many variations of this design were used by Carribean pirates, notably Richard Worley, Emmanuel Wynne, "Calico Jack" Rackham, Edward England and "Black Sam" Bellamy.

It was Bellamy's Jolly Roger flag that became the most popular in the early 1700s. It developed into the standard form for pirates by about 1730, as the individual captains banded together into larger groups, eventually resolving into two major "pirate nations". This is the insignia used by Hollywood for all pirates, regardless of the date or other factors. In reality, Carribean pirates of the 1600s to early 1700s flew insignias of different colors and designs, often involving a skeleton, swords, bleeding hearts and other symbols of violence and death.

So, the skull and crossbones originated with pirates, but has often been used in popular culture without historical accuracy. Pirate ships did not sail around flying a black flag; they only unveiled their true colors when attacking. Mere possession of a pirate flag was enough to send a captain and crew to the gallows, so it would normally be kept hidden.

BTW, the sobriquet Jolly Roger appears to have applied to all pirate flags, not just the skull and crossbones design. It MAY have derived from the French "jolie rouge" (pretty red) in reference to the red flag flown by French pirates. A century after the Golden Age of piracy, the meme became popularized in works such as Treasure Island, Peter Pan, and The Pirates of Penzance.

For further reading, I would suggest Richard Cordingly's "Under the Black Flag" and his edited version of the 1724 classic "A General History of the Murders and Robberies of the Most Notorius Pirates", Angus Konstam's "A History of Piracy", Colin Woodard's highly entertaining "Republic of Pirates", Peter Leeson's acclaimed "The Invisible Hook", and, for a view of early piracy off North Africa, Godfrey Fisher's "Barbary Legend".

EDIT: Thank you all so much for the positive comments and awards! It means a great deal to me, as I am not a professional historian or academic, merely a layperson with a keen interest in the topic.

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So, I'm a merchant sailor somewhere off Bermuda in the age of sail. I see a mast come up over the horizon bearing a black flag with a white skull and crossed bones, do I have reason to panic?

You undoubtedly would! You'd want to turn around and sail as fast as possible in the other direction! Alas, you'd never get the chance! One of the most important aspects of piracy in the so-called Golden Age of Piracy (Late 17th to early 18th century), and indeed with all piracy - is Subterfuge!

If you and and your shipmates had intentions that were less than honourable, it would do you no good to advertise them for all to see from miles around. For the same reason bank robbers don't walk from their home to their intended target wearing a balaclava, with a bag in one hand and a pistol in the other, pirates did not sail around flying pirate colours. Instead they flew false colours; The flag of the nation who's waters they were in most commonly. After all, what better way to get close to a British merchantman than to fly a British flag! There's a phrase (Admittedly dwindling in usage, and largely limited to the US) that comes from this very practice: "Sailing under false colours".

Only once within attacking distance would a pirate ship strike their false colours and fly their true flag. "Why fly a pirate flag at all?" I hear you ask? Intimidation! Sailors would share stories of pirate vessels, and the reputations of their captains and crews would become attached to their iconography, particularly if the crew were known to be brutal in their reprisals. Pirate flags were not to signal to other pirates, or to advertise the allegiance of the vessel. Pirate flags have one very specific audience: The crew of the ship you are actively trying to board.

The sudden reveal within shooting range, the reputation associated with the flag, and the disproportionately heavy armament of pirate vessels for their size all served to scare the target vessel's crew out of fighting. Pirates, like most folk, would rather avoid a fight if possible. Fights are expensive! The ship gets damaged, provisions destroyed, weaponry expended, crewmen injured! Wouldn't it be nicer for everyone involved if this could be settled peacefully?.. Well, at least without a shot being fired!

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Where does the classic pirate flag actually come from? Is it an invention of Hollywood? I know that major pirates like Blackbeard had personal flags with similar themes, but surely pirates wouldn't be organized enough to adopt a universal symbol that says "Yarr, I be a pirate!"

The skull and crossbones has its roots in very real history. The first reference to it under the name "Jolly Roger" comes to us from Charles Johnson's A General History of the Pyrates, a contemporary (Albeit fanciful) account of many of the most prolific pirates of the age. As you said yourself, there were variations upon this theme, and the Jolly Roger was far from universal. Its prominence in modern media likely comes from its simplicity and its very explicit meaning. The Jolly Roger is memorable, easily re-creatable and, for lack of a better word, concise in its messaging. A hanged man, an hourglass, a harpoon through a heart, all of these symbols were used and were tied to the great infamy of their users, but a skull and bones? A child can understand your intentions!

I'm at work, so I may revisit this, as it's a little rushed, but damn it I love pirates! Happy to answer any follow-up questions!