So this might be an obscure problem, but in case I'm not the only one I figured I would post what I've discovered.
I have an 8800GTS vid card, and dual monitors. I like to watch a movie on one screen using VLC, and secondlife on the other screen. The system is a recent upgrade, and since upgrading I seemed to have a very sever graphics stutter across my system when trying to do the video and SL thing. I made sure it wasn't a sata bus problem by playing a video off a usb drive, and another off a mounted dvd image on an ide drive. I tried GDI video instead of directx output in VLC and that got rid of the stutter, but video was only visible on one screen, and no hardware acceleration.
So I was stumped, but on a guess I turned off Vertex Buffer Objects in SL. Walla! No stutter at all! Not only that but it seems to have removed a minor periodic stutter SL was having on its own while panning around. So, if you've got an 8800GTS, you might try turning of VBO and seeing what it does to the smoothness of your framerate.
Hope this helps someone.