I can't get U Tube to skip re-encoding like I used to be able to do. They must of changed their settings, but probably more likely they just re-encode every video now. People used to be able to edit FLV files with a hex editor to trick U Tube into thinking it was a lower bitrate file. By re-encoding every file they prevent people from doing this. After doing some testing and analyzing the files U Tube encoded, I found that it sometimes changes the frame rate slightly. I had it change 29.97 to 29.937 and 23.976 to 23.943. It didn't do it all the time, but it didn't seem to affect the playback to me.
I have seen many people's videos play choppy, frequently the SD version only when its a HD upload. Also, if it is HD and you click HD when the video is already playing, it frequently plays choppy. You can avoid the choppy playback by either hitting the HD button before the video starts playing, scrub the playhead to the beginning after hitting HD, or adding &fmt=22 to the end of the URL. Not sure what to do about choppy SD video playback though. I'll have to find a choppy SD video sometime and analyze it.
Interestinly, U Tube states this for their file formats list:
• .MP4 (ipod/psp)
• .MKV (h.264)
Seems like they want MKVs instead, not that it should really matter though. They use x264 with mencoder to encode anyways. But some people on Doom9 have stated they've had better success uploading in MKVs instead of MP4s. I'll try using MKV for my next several videos I guess.
If anyone is curious, here is an analysis of a video from U Tube I got from MediaInfo (used spoiler since it is a little long).
Insert clever text/image here.