Okay, so you overtake a ship, defeat its martial defenders and take its captain prisoner. Its a beautiful ship and seems like something you might want to sell or possibly even add to your fleet... but there's like 30 or 40 of these innocents standing around. How do you deal with crew who surrender?
All obviously can't secretly be hoping for a life of piracy, serving alongside the very men who just killed their friends and ship-mates. Feeding and caring for them indefinitely is too expensive. Marooning them is pretty much the same as slitting their throats and dumping them into the sea. They won't be worth much as ransom, and simply releasing them onto the docks will only cause problems as they seek out law enforcement, their employers or plot revenge...
I'd be interested to know what everyone did with the opposing crew - or did your GM just treat them as background noise?
Depends on what type of pirate you are.
If you are the scurvy dog type, you suggested it yourself.. slit their throats.
If you are more of a good type, offer them employment, til you hit the next port. Even if they don't want to 100% be there, odds are they would accept gainful employment til the next port; especially if you are treating them well.
Otherwise, if they reject the employment, you really can't trust them, so it's a tough situation. Marooning them might be the only option.
Well there is not much in the way of law enforcement in the shackles. So that remains an option. Heck if the are sufficently scared they can spread your legend. If you capture a ship with slaves offer the slaves a place in your crew and let them know once they have dealt with their former masters you can set sail.
The last time my group and I took over some dudes, we gave them the option to stay where they're at (island or whatever) or join us. When we were down to a handful left, we thought it would be fun to have them battle it out and the survivor gets to join.
It was my idea and I figured that it would weed out the weaker sailors and leave us with a superior fighting force. Our DM had each of us play a sailor, and he threw 2 daggers in the middle. it was a fun little mini-game and he thought the whole thing was ridiculous.
My players have handled it in an interesting way. For most crews, they simply ransom them at Bloodcove or some other port that has a ransom broker. They are worth a reasonable amount and they will be stopping at port anyway. They make a check to recruit like they would at any port, and those that accept are inducted into the crew. Those that decline are bound in the hold and fed sparsely until they make it to port, where they are ransomed.
Now, the captain in my players group is a Tiefling from Cheliax, and the bastard son of a member of the Thrune family. He HATES Cheliax for their treatment of his kind. So for Chellish crews, he gives them a single opportunity to turn and fight against their brethren, and if they refuse they are executed and thrown overboard.
I think it's something of an interesting way to handle it.