SodaConstructor allows you to create and modify objects using "joints", "springs" and "muscles" and then animate them to see how they move.
Rader's BIOLOGY4KIDS offers basic information on biology in a colorful, accessible format. The same people host Rader's CHEM4KIDS, Rader's GEOGRAPHY4KIDS which also offers Earth Science, and Rader's Numbernut.com, a math games site. Numbernut is a new site, so some of the content may not be online yet.
More formal than the other sites, Project Logged On is a science curriculum designed by the Curry School of Education at the University of Virginia. It offers project-based curricula for middle and high school students. For example, "The sixth grade case-based curriculum offers an in-depth look at the scientific inquiry method. Each of four cases is devoted to one or two aspects of the scientific method. Cases are open-ended and based on questioning urban legends. Students are provided an opportunity to experience the scientific method first-hand through inquiry exercises, data collection and analysis, and experimental design. The curriculum challenges students to question, hypothesize, and explore the process of arriving at possible conclusions. Students will become proficient in the various steps of the scientific method and hence, become confident in implementing them in new situations." The curricula appear to be free but I haven't delved really deeply into this one yet.