What browser are you using? If you're using Chrome, you can try disabling Chrome's built in Flash Player and using the stand alone version. I believe Xemnas posted instructions for this somewhere...
Edit:
Quote from sylfaen;932107:
Have you tried enabling/disabling hardware acceleration on the YouTube videos?
You can toggle this setting when you right-click a YouTube video and visit Settings in the resulting context menu.
Also if you're using Google Chrome, someone suggested disabling the Pepper Flash Player.
[Image: http://puu.sh/R03T]
This can be accomplished by entering [chrome://plugins] (minus the brackets) into your address bar and clicking Disable for the item seen above.
Other than that, I believe that would truly be the lats of what I could suggest.
Related Link
Here is an unanswered question on the Google Product Forums:
http://productforums.google.com/forum/#!topicsearchin/youtube/shaky$20OR$20controls/youtube/_XLSb8o1RCM
It may or may not be answered sometime in the near future.