I am not opposed to having a little fun with the themes that come with certain team names. Fortunately there is no one to really offend by using the theme that comes with the Pirates.
However, I've never really been a fan of the phrase, "let's raise the Jolly Roger." I don't know, for me it always just sounds a little too jolly. I'm not sure when they started using it in Pittsburgh.
There are multiple variations of origins for the phrase "Jolly Roger" describing the skull and crossbones flag, or just a simple black flag.
There are also numerous unsavory meanings for the phrase, none of which a fan can be very proud.
For me something a little more menacing like, Hoist the Skull and Bones is a little more suitable, and carries with it a certain menacing threat.
I have never had the honor of attending a game at PNC park so I do not know the sorts of cheering that goes on.
I think a really interesting cheer for the fans to to take part in would be when a player makes a good defensive play, to in unison give a deep and hardy "Arrrghh!!" Seem silly? If you doubt me try it for you self.
Try squinting one eye, give yourself a twisted grin, and with your best pirate drawl, growl out 'Arrrghh!" Now imagine 15,000 fans doing it at the same time.
Similarly, if there is a bad call by an umpire or an unfortunate play, the fans can let out a bitter, "Gaarr!"
A nice promotional might be to put and "X" Marks the Spot in the center field stands and let it be a home run target for Pirate batters to aim for, with canon fire (simulated sound effect) to announce a hit.
A famous quote delivered in one form or another by different people says, "Where there is sea, there are Pirates." The Pirates have a long and storied history. They have been around baseball for more than 100 years. This should become the mantra of the Pirates, modified as the title of the story above suggests.
The Pirate mascots, Pirate Parrot and Captain Jolly Roger, are largely for the kids, and that is fine. Leave the name Jolly Roger to the Captain, and let's raise the skull and crossbones.