Science teacher have it tough. They have one of the most costly subjects in a school to teach, yet get a very small budget. In my website of links to good software I have things like virtual lab, Phet and Phun that can simulate some experiments, but are mostly focused on Physics. I have recently come across HHMI Biointeractive. This focuses on high end biology, and directs students through simulations commonly done in high end labs. Being a primary teacher means that a lot of this is beyond my background knowledge, but it looks like it covers many of the topics in year 11 and 12.
For a lower stage of learning there is Science Lab by Schlumberger - a range of interative applets that let students experiment with things like trains for the dopler effect.
I keep looking for great science web ages, Java/Flash applets, but if you have a favourite that I haven't found yet, please drop me a line.