When I was a middle school science teacher, I regularly used online simulations to enhance understanding of the topics we were studying. While a simulation can't (and shouldn't) replace hands-on activities in science class, there are some topics that are just too dangerous, or impractical, or on the wrong scale (too big or too small) for students to manipulate first hand. Other topics are too complex, and a simulation might help simplify the situation.
The Outbreak at Watersedge is a great simulation in this sense. It is an interactive game that simulates a public health crisis in the fictional town of Watersedge. The player takes on a role as an intern in the Watersedge Department of Health. The director of the Department sends the player on errands to take pictures, collect water samples, interview people, and map out incidents of illness to try and figure out why people are getting sick. It's a pretty well-developed simulation, and since it is narrative-based, it is fairly immersive. I'd say it would work well for the middle school crowd in particular, but it could be used for precocious upper elementary students as well.
Of course, no simulation is going to be a perfect fit for every classroom or curriculum. This simulation is a great way to understand how diseases are spread, and what causes epidemics, so it would probably fit best in a unit on disease and immunity or perhaps a science-and-society unit. It gives some practice in thinking scientifically, eliminating possibilities, and basing inferences on data and observations. This could be a great supplement to a science unit you teach!