One of the best websites for science simulations is PhET from the University of Colorado at Boulder. Originally founded by Physics Nobel Prize laureate Carl Weiman, PhET provides fun, interactive, research-based ( simulations of physical phenomena for free.
Teachers can access the Teacher Ideas & Activities page for teacher-submitted contributions, designed to be used in conjunction with the simulations.
Some Sources for Science Simulations
Biology Online Labs
Anatomy Online Labs
Chemistry Online Labs
Geology Online Labs