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Since this helped others, I figured I would post this here.

If you are running a DirectX 9.0 card, you can possibly reduce stuttering by running in DirectX 8.1 mode. To do so, add the line -dxlevel 81 under TF2's launch options. Alternatively, you can enter mat_dxlevel 81 in the game's console. The graphical difference to my knowledge is less bumpy specular (shiny) maps as well as slightly different looking water.

Also, you can limit TF2's frame rate output by adding +fps_max # to your launch options, substituting # with the number of frames you want rendered per second. TF2's default is fps_max 300. Setting this to a lower number will help smooth out large fluctuations in frame rate. I recommend starting at 150 and seeing if it improves your performance.