Check out the minecraftinschool wiki created by Lucas Gillispie (a former student in the MIT program at UNCW). This blog discusses how to set up minecraft for your classroom, provides sample projects, lessons plans, and even has sample student projects. This is very well done and I encourage you to check it out: http://minecraftinschool.pbworks.com/w/page/37244189/FrontPage
Here is just one of the many videos Lucas has created for minecraft in his classroom (many more on the page above)
For those that are new to minecraft, check out this video: