Two good ones:
The two activities that I (and my kids) liked were on the Alive Maths site from McMaster University. The first was "Lulu" and the second was "Spiral". Lulu presents a cartesian coordinate system where you and Lulu are in different places. Lulu moves when you do, following certain rules (e.g., when you move up one, she moves two left.) You move, trying to meet up with Lulu. The second activity, Spiral, allows you to set distances and angles to see what types of spirals result.
I liked these activities because they are open-ended and exploratory. They could be used both with younger and older students.
Two not-so-good ones:
Two sites that I was less impressed with are the Genetic Science Learning Centre from the University of Utah, and The Last Straw: Plants and Water Stress from Cornell University. The section of the Genetic Science Learning Centre site that I viewed was basically an animated textbook, and as result, it was not interative enough.
On The Last Straw site, the levels of the two main sections seem to be different. The text of the tutorial seems to be too high for the stated grade levels (grades 3 - 8), while the simulation is too basic.
References
Alive Maths. http://tapor1.mcmaster.ca/~sgs/maths/
ENC Clearinghouse. http://www.enc.org/weblinks/classroom/simulations/?ls=sn Genetic Science Learning Center. http://gslc.genetics.utah.edu/
The Last Straw. http://cycas.cornell.edu/ebp/projects/laststraw/ise/home.html