The iPhone 3GS with the firmware that was released in September, I forget the version was the first time any personal device could play Handbrake's Apple TV present.
The iPad will be more powerful so if you have encoded your movies with that you should be fine. I've got a huge folder of 720p MKV's waiting to be encoded. When it's released we'll find out the best settings to max it for iPad and Apple TV.
There's a discussion on the Handbrake forum.