Yes I know what you are thinking. Would I not lose the quality? Well, I cannot really see a difference between the source and the MP4 output. Doesn't mean that there is not, but it is not worth worrying about.
There is one little issue though. There is a max file size limitation for MP4 files it seems. Maybe there are apps that can player larger MP4 files, but te standard size is 4GB max. Zune Player wouldn't play anything larger.
I am using Handbrake to transcode the videos. I do 2-pass conversion with turbo 1st pass, and set the output filesize to 4GB. That makes video files generally if the size 3.9GB. But there were two video files so far that came out as 4.1GB and they were not playable.
I've been transcoding videos for 3 days straight. Man I wish I had a Sandybridge CPU with quicksync. Problem would be that Handbrake doesn't support quicksync yet. It should. I don't know if this is a software issue or a codec issue. All I know is that they should get it to work FAST.