Pedagogica - a very cool piece of software to explore genetics, some chemistry, and some physics. Download and unzip and then run the file titled 'workspace.jar'. Choose your folder of interest (biologica, chemica, connected chemistry or dynamica) and dig in! The original download page can be found here in case the above link does not work.
VGL II - use this software to solve various computer generated genetic problems.
Aipotu - explore genetics and its associated biochemistry and molecular biology via a problem-solving approach.