Starting on May 1, 2009, penguins who were Secret Agents and/or Tour Guides began to receive 250 coins per job each month for doing their "jobs". Their salaries are paid through Penguin Mail. This information was first confirmed by Billybob, and later by The Club Penguin Times (found in issue #184). Income for both jobs can be received, so penguins who are both a Secret Agent and a Tour Guide can collect a total of 500 coins each month.
Ninjas are not paid, as they don't do a service important enough to warrant a salary. As of December 1, 2010, EPF (which is now 350 coins for EPF only) agents started getting paid after a bug that had the postcard a message from "Sys" saying "I Met Rockhopper!".
The Rescue Squad, Pizza Chefs, Coffee Waiters, Lifeguards, Puffle Shop staff, and Firemen are all not paid a salary. This might be because the EPF is very crucial to Club Penguin, and the Tour Guides show new Penguins around the island. The jobs that don't receive a salary are all important, but are just not crucial enough to the island, at least for now. You can still get paid even when you don't go on Club Penguin.