The Physics Aviary - my "go to" site. Includes the Quick Graphing Tool my students use all year long! (Free)

ExploreLearning Gizmos - nice introductory simulations, but can also use to record data ($)

The Physics Classroom - textbook-like that includes various simulations and also practice problems. (Mostly free)

oPhysics - another great simulation site. Also includes a drawing program.

pHet Online Simulations - the "grand-daddy" of them all (Free)