Prodigy is a game that I have been using with my own kids for about a year now and I have been super pleased with, but up until now it has only been accessible through the website. Prodigy has now come out with an App for the iPad that works both online and off, which is a huge bonus.
The game itself has the student create an avatar and traverse a magical land, meeting different guides who give them various tasks to complete. During these adventures, the students have to complete math problems to battle the creatures they encounter.
As a teacher I can set up my class view their progress and any areas of difficulty. I can assign "homework" for my students to "complete". What's great about this is that the students don't even realize that they are doing an assignment. The math content that I assign, say "addition of three digit numbers with carrying over", is woven directly into the game. Once they have completed the specific math problems assigned Prodigy gives them problems from other areas of math at their level.
They game is very engaging and kids, as far as I've seen, play much more after their assigned "homework".