This happens with every video I upload or that I watch on any website that uses the Flash player for playback, which unfortunately is most of them. Videos stutter like crazy. This video I did in After Effects is a good example since the stutter is very noticeable: http://www.youtube.com/watch?v=TmP0HRG2lYE&feature=youtu.be&hd=1
No matter the browser, the video looks terrible as far as motion goes, stuttering all the time. I'm not talking about buffering problems, even with the video buffered all the way through it still stutters. Obviously this video plays perfectly fine in my computer, and given that I have a GTX770 card with 4 GB of RAM I know hardware is not the issue. And yes, hardware acceleration is enabled in the Flash player plugin.
For years I was never able to play any video on websites without this horrible stutter, I always had to download them and watch them in VLC or other program to watch it free of stutter. And I can confirm that this stutter is because of Flash technology, because I just set You Tube to use the HTML 5 player by default and it plays perfectly fine.
So I keep wondering, what is it about Flash player technology that makes videos stutter so much?