Re. PeteBoom's post above, the First Rate that went down in Plymouth Harbour was the "Royal George". There is still a legend that the ship was being canted to clean the copper on one side, the gunports on the other went under and that was that. However, it is equally possible that, with all the rot and damage from marine creatures, canting the ship caused the deck beams te break away from the ribs and frames, and the effect would be the same.

Re. Grab's post on the "Mary Rose", when built she was quite well designed. Unfortunately, in the thirty years which passed between her launch and loss, the Royal Shipyards, at Henry VIII's behest added lots of cannon, which, with the necessary extra frames, raised her Centre of Gravity. Even this wasn't enough to ensure her doom, until she put to sea with a Vice-Admiral embarked. To maintain the dignity (and safety) of the said Vice-Admiral, she carried two hundred or so extra men-at-arms, bowmen and arquebusiers, all mustered on the upper deck and quarter deck. This tipped the balance between being merely unseaworthy and a menace to all who sailed in her. There was a program about this on BBC2 about a year ago.

However, as more than one poster has mentioned, the one, three or even nine holes a love-lorn cabin-boy could inflict pale into insignificance beside the damage of which a boring (that's "drilling", not "tedious") mollusc named Teredo was capable. Before coppering was introduced, they could turn a ship's timbers into Gruyere cheese over a couple of decades.