Here is a list of iPad activities for upper elementary/middle school students. Most of the apps listed are free. When using this in my classroom, I left this list at an iPad center, and had students choose an activity they wanted to do. To ensure they were learning, rather than just playing or surfing the web, I required them to do a one paragraph write up about what they did during their iPad time. Some of these activities already require some sort of work to be turned in. If that is the case, I let that take the place of their write up.
This can be left at an iPad center, or used as a reference page for teachers.