Emulator Problem: Recording videos in HD

I'm using JNES and I'm interested in recording videos to HD format. Help with other emulators doing the following would be great too.

What codec should I use when changing .jmv to a video file to the .avi insuring the best quality. I'm trying to get the best quality for youtube and seem to be missing something.

I know how to make HD videos using Windows Movie Maker, I also use Total Video Convertor to make the size less. When converting using this, what option should I select
 
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