If you want to tune a workstation, or create a killer Quake III box, you will want to pay attention to the video subsystem and see how well it performs. For 2D applications, you can test the system using x11perf. This program will perform a variety of tests using the X server and drivers. Since it is designed for performance testing, it is designed to run each test five times, then take the average. The machine should have no other users or activity going on, and you should disable the screen saver. You can disable the screensaver either with the command xset s off or by killing the process called "xscreensaver". You may need to run both commands in order to turn off the screen saver.
Testing with x11perf will take several hours depending on the speed of your CPU and graphics card. Once complete, you will have a log file that you can then compare against other machines that have also done testing, or against a baseline test you ran before tuning to see if the X server speed has been improved. To do this comparison, you can use x11perfcomp to compare two or more tests. Higher numbers are better, as the resulting numbers are in terms of objects per second.
You can test out 3D performance using applications like Quake III, that run the application through a set world and events, most of which will stress the system. Mark down the resolution, bit depth, and frames per second reported from Quake III, and you now have a baseline to work from.
A caveat to using Quake or 3D applications is that this is testing more than the video card. Other subsystems, like the CPU, video drivers, GLX (3D) drivers, and memory are also tested. If you want to use this method for comparing speed, you should also be sure the other subsystems are tuned as well.