Hacked by a Pirate

Whenever a character, be it the Asian and Nerdy hero or the computer genius villain, decides to hack into the opponent's computer and mess up with his plans, he'll never stop at just making the computer malfunction. You've got to do it with style.

And so, a Skull and Crossbones image shall take the entire screen of the hacked computer, possibly followed by the voice of the hacker laughing in the background. Alternatively, an 8Bit image of the character doing the hacking, or his logo, or perhaps a mix of the above, shall appear on the screen, such as a Skull and Crossbones, only the skull is wearing the very same hat the hacker wears.

Named after the fact that Skull and Crossbones happen to be the Pirate's symbol of choice. Note that the trope is rarely, if ever, performed by an actual pirate, since they usually try not to be noticed.

Examples of Hacked by a Pirate include:

Anime and Manga

The lead character of Bloody Monday Fujimaru, known as 'Falcon', always leaves his personal symbol of a diving falcon at the screen of every computer he visits as a calling card.
Radical Edward from Cowboy Bebop tends to do this. Although Ed's more into smiley faces and other sillyness.
In Yu-Gi-Oh!, Pegasus does this by showing his favorite cartoon rabbit character when he counter-hacks Kaiba trying to hack into his system.

Comic Books

In V for Vendetta, V has actually been manipulating the Fate computer for years. The "pirate flag" is just the final stroke to drive the Leader completely over the edge.

Film

Independence Day, of course. One must wonder how the alien civilization viewed the chuckling skull-and-crossbones - would it be too culturally specific to understand, or would it be something universal in ominous meaning?
- Since the skull is obviously human, it would probably be more shocking. Humans posed about zero threat to them up to that point.
The famous "Ah, ah, ah. You didn't say the magic word." in Jurassic Park was a justified example, as it was a hacker's defense against someone else trying to hack his computer... and a really crappy hacking attempt.
Happens like that in Tanguy when the title character's father sends a virus to his PC. The words "I Love You" (name of a notorious virus back then) flash on the computer screen along with a skull.
The brief glimmer of hope that was the hacking scene in Battle Royale featured a chibi-style basketball player dominating the monitors at BR headquarters.
All over the place in Hackers. The viruses launched by the hackers all have some malicious and/or cute animation that's displayed while they're mucking about in the system

Newspaper Comics

Oliver Wendell Jones once caused global chaos—cities in flames—by posting on a stock market computer the message "Avast, ye scurvy corporate swabs! Bank of America is about to go belly up!"

Video Games

In Geist, ghost Raimi can possess a computer and cause it to flash the skull-and-crossbones, pretending to be a virus to scare a technician.
The Jawbone virus in the Purple Moon computer games. Expanded Universe material goes out of its way to say that this is the only thing it does, as while invading the computer of the local equivalent of Bill Gates is not beyond Bo, doing actual harm is.

Web Animation

Invoked in Red vs. Blue: Reconstruction. As Simmons tries to hack Command's computer system, Grif unhelpfully offers advice such as, "You should try uploading a virus to the mainframe. I find viruses that feature a laughing skull work the best."

Web Comics

Unwinder of Tall Comics discusses his idea for hacker identity with Amy, who actually is a hacker:

Unwinder: I'd call myself "Maestro". My thing would be that when I hacked a website, it would play classical music. I'd refer to the songs as "1337motifs".
Amy: You wouldn't last five minutes.

Web Original

Mocked in Something Awful's "Virtual Intrugue - An Internet Adventure"

Western Animation

An episode of Archer had the ISIS computer system infected by a virus that displayed an actual pirate complete with parrot which sang "Hunch, hunch! What, what!".

Real Life

TV Tropes was once hacked and replaced by this sort of showman. (Memory of this event has been somewhat superseded by The Great Crash roughly a month later.)
Such practices of depicting hackers using fancy graphics/logos to identify themselves most likely originated with software pirate groups way back in the 80's - who typically did have some form of ASCII based logo that they would insert into the game they cracked and released. Even today, it's common to find such logos/art in the .nfo file that often accompanies such pirated software. With Hollywood being Hollywood, it's no surprise that they have no concept of the difference between a hacker and a pirate.
YouTube has a few videos with virus pranks. One of them involves a skull animation.