Get Fuzzy and PoTC

Get Fuzzy mentions the Vasa here and here.

It's a warship, not a pirate ship, but it is a historic ship.

Which sank shortly after it was launched.

In Pirates III (At Worlds End), Jack realizes that they need to escape Davy Jones's Locker by turning the Black Pearl upside down at sunset. He does this by running back and forth on the deck. The others join him and Barbossa cuts loose the cannons so that they can roll back and forth, also.

The captain of the Vasa did something similar before the ship was launched. Thirty men run back and forth across the deck. The ship began to rock after only three passes. They quickly stopped for fear of sinking the ship.

When the Vasa was officially launched a gust of wind caught it and pushed it over. The cannon ports were open in preparation for firing a salute. Water poured in the ports and the ship sank. Many of the crew including the captain were killed.

The inquest into the sinking was a tricky thing. The real problem lay in the design but the king, Gustavus Adolphus, had been involved in the design and questioning any decision of the king was considered punishable.