I don't see much difference in quality, but of course it comes down to rendering it out in h.264 or in lossless avi (Huge File)
bit rate and the such
Remember though how bad youtube will crush all quality, i myself use WMV over H.264 it has a better black depth, just a little bit bigger in file size.

That wmv don't look right? got a pixel dust look to it.
for me FCP Mp4 Convert looks the best.

I am still rocking my PVR from OG skate days.
5 years ago i did a test.. ;/

Wmv upscale 10mbs 320kbps ac3 ect..