Bioman Biology is a nice resource that I learned about from David Andrade. On Bioman Biology you will find dozens of educational games and virtual labs designed to help students learn about topics related to biology. The games and virtual labs are organized into eight topics; physiology, cells, ecology, genetics, classification, life chemistry, respiration, and scientific methods. Most the games are Flash-based but a handful of them are available as free iPad apps. The games and virtual labs are appropriate for middle school students.
Applications for Education
Bioman Biology offers you the option to track your students' game scores. To do this you have to register as a teacher. Then when your students complete a game they have the option to enter your email address and have their scores sent to you. Your students do not need to have email addresses of their own in order to send scores to you.