When ye be thinking of pirates, ye be most likely picturing an image not unlike the one above. This be a pirate flag, or more properly, a Jolly Roger (that's it for me writing like a pirate...I won't put you through the torture of reading more). The image of the skull over two crossed blades belonged to John Rackam, who was a terrible a pirate, a term which here means he was an incredibly crappy pirate. In fact he is only remembered for two things: the two women he had as part of his crew, and coming up with the coolest-looking Jolly Roger.
This somewhat weird/goofy-looking Jolly Roger was about the worst thing you could have seen on the open seas, as it belonged to none other than Edward Teach, a rogue who you might know better as Blackbeard. His flag illustrates the point that Jolly Rogers had all sorts of designs, although most incorporated skeletons.
The black background seen in most Jolly Rogers is not an arbitrary choice. If a ship was pursuing you and it raised a black flag that signified that should you and your crew surrender your vessel with no resistance, you would be given quarter. If, however the ship pursuing you flew a red flag it was time to crap your pants, because that meant the pirates chasing you down were about to attack your vessel with no mercy. There would be no quarter given.
Of course the rainbow Jolly Roger meant things were about to get fabulous!
So why were these fearsome flags given such a seemingly innocuous name? There are three possibilities. First, "roger" was an old English term for "vagabond" so the name could have had reference to the criminal nature of pirates.
The second possibility is that the name is a corruption of the French term jolie rouge which meant "pretty red" although the fact that Jolly Rogers signified an impending attack, as opposed to an impending retreat it is unlikely that the term was derived from anything remotely French.
An example of a French Jolly Roger.
The final possibility is that the term was derived an old English nickname for Satan, "Old Roger". I find myself wanting to believe this last possibility because, frankly, it's so incredibly awesome. Also, this knowledge makes incredibly wary of anyone with the name Roger or Rogers. Especially if they are old.