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As others already said, the Apple TV preset in Handbrake is a top notch conversion for the iPad.
However, once I discovered the Airvideo app and its free desktop server, I stopped using Handbrake.
Airvideo will either convert for later syncing or convert on the fly and stream over your own wifi network or over the internet to anywhere you access it from (including 3G but that would get expensive quickly with a limited data plan.) For offline conversion you can queue several files.
It handles any format you throw at it including high definition mkv, flv (flash video,) avi, divx, xvid, etc. You can set the size and quality of conversion but it streams so well I've just left mine maxed.
The streaming is impressive with no hiccups over any relatively steady connection. It just buffers ~10-15 seconds at the beginning and works perfectly after that.
Its conversion speed also beats Handbrake hands down.
They have a free version you can demo so nothing to loose.
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