Are you specifically looking for conversion to mp4/m4v or just want to watch videos on your iPad?
If it's latter, you can get
Air Video. I believe they support iPad already. I don't own an iPad yet (Canada, so close... yet so far), but I do have an iPod Touch. I can watch any videos on my iPod Touch streamed from my PC and Macbook with live conversion with Air Video.
What's great about this app is, not only does it convert any types of videos encoding (so far, I've watched videos encoded in AVI, MPEG, DivX, MKV, and many other types), I can even travel to other places with wifi connections and watch videos hosted on my home PC/Mac remotely.
I think if this combine with remote desktop apps like LogMeIn, you can just remotely download movies at home, and then watch it where ever you are in the world with iPad.
If this is not what you're looking for, then VUZE sounds good to me.
🙂