Many have suggested that some choppy playback issues (for in-browser playback) are related to the Adobe Flash plugin.
Adobe has released a new version of the Flash plugin this week, which may perform better (although I can't confirm that the problem has gone away completely).
Here are some steps to follow to cleanly update your Flash:
1) Download the Flash plugin un-installer from Abobe, available at:
http://kb2.adobe.com/cps/141/tn_14157.html
2) Close all browsers on your machine and run the Abobe Flash plugin un-installer you downloaded for your platform.
3) Open your browser and reinstall the Adobe Flash plugin (v.10.0.42.34 or greater), available from Adobe at:
http://get.adobe.com/flashplayer/
4) After the installation, close and re-open your browser, then try playing back some Flash video at YouTube or wherever...
Hopefully this works. Good luck.