MP4 and M4V!
There really is no difference between MP4 and M4V, but M4V files automatically load in iTunes. Handbrake lets you create either an M4V or an MP4. If you get an MP4 file however, you can easily change it into an M4V to make it iTunes-friendly. There is no conversion necessary because it is already using the right codecs. You just have to change the extension. Double-clicking on an M4V will load iTunes, but it is still possible to open it in QuickTime.