YouTube re-compresses anything you send them. Best thing to do is to use h264 and set it to their pixel dimensions and then compress it only enough so that it ends up being under their limit of 100 mb. Then you are starting with the best image quality you can have prior to their compression. that should help a lot.

Mark has it right.

Target the you tube size which is 320x240 @30fps. Try to run your compression as close to the 100Mb limit as possible so as to give them the best quality piece to convert from.

I usually work in 720x480 or 720x486 then after my final is done, I pop it into a 320x240 container and render it out for final posting. Do a scale down and any final color correction you feel is needed.

Here is a video I did for the Ohio Film Commision.

www.youtube.com/watch

Not the greatest quality but still acceptable,it was uploaded to you tube by the client as a WMV that was 640x480 so there is a slight stretch due to aspect ratio being off a bit. This means it went through double compression and it does show.

One thing I would ask is what codec are you using to store your initial files with quicktime? Just because you are using quicktime does not mean you are getting lossless storeage in your MOV file.

For draft work I render to motion JPEG-B with a compression ratio set to 92%. This gives good quality and manageable file size. But for my final render, I use ANIMATION codec set to 92%. This generally will not play smoothly on my computer, I simply use it as a master for creating the deliverable (ie H264, FLV, DVD) via quicktime pro. I also keep a companion H264 copy of the same file in the same folder for viewing purposes.