Graylo of Gray Matter has written a long article about using SimCraft to model DPS and spell rotations in his moonkin. Note that this system is used for most of the classes in WOW and that Graylo's tips are only good for those using Windows. He does give links that will help you if you don't fall into those categories.
http://graymatterwow.blogspot.com/2009/10/moonkin-tools-simcraft.html
UPDATE: WOW Insider describes how to use SimCraft (or SimulationCraft) here.
http://www.wow.com/2010/02/01/blood-pact-using-simulationcraft-for-gear-selection/
***************************
Copyright Solo MMO Player at http://solommo.blogspot.com