That depends on the pirate in question. As far as walking the plank goes, that almost never happened, to merchants or pirates. There are only two documented accounts of it being done by pirates. Once by Stede Bonnet and again after the golden age was over. Stede Bonnet was invested in the mythology of piracy and did a lot of things that weren't typically done by other - more successful - pirate captains.

If someone was to be thrown overboard most pirate captives (and these were usually crew members that broke their laws) were bound, cut, and thrown over the railing. If someone was to be marooned they were sometimes thrown overboard unbound near an island, and other times towed ashore. Setting up a plank to walk was a lot of needless work toward the same end and is really only found in the works of Howard Pyle (take a look here) or Disney.

To answer what pirates actually did with their captives depends on the pirates and the captives themselves. Most pirates operated on a very simple philosophy. They wanted the goods aboard a ship and sometimes the ship itself, not the danger and hassle of a fight. If the captain stopped and surrendered when they raised the Jolly Roger, didn't put up a fight when the pirates boarded and handed over the manifest there was usually no danger to the crew. If the haul was rich some pirate captains would even overlook private stashes of regular sailors pay. They were usually formerly regular sailors themselves after all.

Now you weren't entirely out of danger though. Some pirates would offer to take any crewman that wanted out of the regular seaman's life a place on their crew. A number of young, adventure-minded sailors took them up on the offer. However, if they were light on crew or were in need of a sailor skilled in a certain aspect of life aboard a ship, the pirates were likely to kidnap regular crew. Two excellent sources on this are: If a Pirate I Must Be by Richard Sanders and At the Point of a Cutlass by Gregory N. Flemming . Cooks, surgeons, carpenters and pilots were at particular risk.

If the pirates wanted your ship there were a few possibilities. First, they might just trade up. Give the merchant crew their vessel and take the larger one. After moving over stores, guns and personal affects. If they wanted both ships, say when Blackbeard was amassing what he wanted to be a pirate armada, there was usually a small pinnace in tow that could ferry the merchant crew to port.

However, these mostly peaceful interactions only took place between friendly peoples. If an English pirate took an English ship they were likely to be cordial toward each other. Most French and Dutch ships were relatively safe as well. Spanish vessels, if they were unguarded, didn't always fare as well. The Protestant leanings of most pirates, and the fact that the Spanish were less than friendly toward the incursion of foreigners in what the pope had declared their sole holdings from (the 1494 Treaty of Tordesillas meant that many pirates would happily kill any Spanish crews that they captured.

Some pirates held resentments, grudges, or hatred toward certain people as well. Bartholemew 'Black Bart' Roberts is a famous example. After he had been slighted by residents of Barbados and Martinique (in his view) he changed his flag to a likeness of himself standing atop two skulls. They were labeled ABH and AMH, for a Barbadian head and a Martinique head. He made good on his threat whenever the opportunity arose.

Some pirates were actually as brutal as the mythology claims too. Usually early in their career, when they were striving to make a name for themselves, some would kill entire crews. Probably the most famously brutal Pirate was a buccaneer named Francois l'Ollonais. He was known and feared for unnecessary torture and murder. In Empire of Blue Water by Stephan Talty the author calls l'Ollonais a sociopath and a ruthless killer. He was fond of flaying, burning, the rack, and woolding - the process of wrapping a prisoners head with rope attached to a piece of wood and twisting said wood until the victim's eyes burst from their head. He even went so far as to lick his blade clean when he killed a Spanish executioner sent against him.

Sorry for the long post. Hopefully it got around to answering your question. If you want more on the topic I do a podcast on pirates and did an episode about this:

http://piratehistorypodcast.com/?p=435

If you're looking for further reading my sources are:

The Buccaneers of America by Alexander O. Exquemelin

A General History of Pirates by Captain Charles Johnson

The Invisible Hook by Peter T. Leeson

The Pirates' Pact by Douglas R. Burgess Jr.