Handbrake.
I converted 7 episodes of Lost which were 720p MKV files by using the Apple Universal Preset. It took a while to do one on my Mini if i'm honest, but I set a batch off just as I went to bed so it was all done in the morning.
Does anyone have directions for encoding HD video from a camcorder to an ipad using handbrake? I could not find any instructions. I'm using the direct AVCHD source from my canon camcorders hard drive.