OK, I don't know if this has been posted here before, but here is Canon (Canada)'s procedure provided to customers for doing focus tests. I received it from Canon after complaining about AF problems with a lens. I suppose the same procedure would apply to bodies too. I think it is a useful list, for starters at least.
===============
BASIC SLR FOCUS TEST
===============
In order to isolate the issue that you are experiencing, we suggest performing the following focusing test and responding with the results. Due to the large number of factors that can affect focus, it is imperative that all of the settings below be adhered to in order to properly assess the situation.
1. If you use filters with your lenses please remove them for this test.
2. Use the “Clear all camera settings” and “Clear all Custom Functions” of the camera to reset the camera to its default factory settings.
3. If your camera offers the AF microadjustment feature, please ensure that it is disabled for the purposes of this test.
4. Set the Image Quality setting to "Large JPEG" (or preferably RAW if possible)
5. Set the "Picture Style" to "Standard".
6. Set the shooting mode to "aperture priority <Av>" and set the aperture to the maximum value possible (smallest f/stop) however please also ensure that it is not set any lower than f/2.8
7. Set the "ISO" speed to "100".
8. Set the "AF mode" to "One Shot". For this test, do NOT use "AI Servo" or "AI Focus" modes.
9. Set the "Drive Mode" to "Single Shot". For this test, do NOT use "Continuous" shooting mode.
10. Select only the centre auto-focus point.
11. If you use a tripod, please disable the Image Stabilization of the lens by moving the "Stabilizer" switch on the lens to the "OFF" position.
12. Place three objects of the same size on a table at different distances from the camera. From left to right, place the left most object closest to the camera and the right most object furthest from the camera. From front to back, space the objects out by about 2 to 3 inches. For easier analysis, we recommend using objects that contain text or writing on them and that contain a fair amount of contrast (i.e. avoid using objects that are completely one colour).
13. Compose or frame the image in the viewfinder so that the three objects occupy and fill as much of the frame as possible.
14. Use the centre auto-focus point to achieve focus on the centre object and then, without re-framing, capture the image. Please ensure that the centre AF point is aimed towards a part of the object that contains contrast (i.e. avoid having the AF point land on a part of the object that is completely one colour).
15. Please ensure that there is more than adequate lighting in the room. If possible this test should be performed outdoors in full daylight.
16. Please ensure that the lens is "de-focused" or purposely thrown out of focus in between every test shot. To do this, focus on an object that is located at a different distance to your intended subject and then re-perform the test.
17. Optional: redo steps 1-16 using the "Live View Shooting" feature of your camera (if available on your model). This will help isolate the issue even further.
Note that, after downloading images to your computer from a digital camera, it is tempting to magnify or print out just a part of the image once downloaded to your computer. This can magnify small errors in AF that would otherwise not be apparent when being viewed at a more traditional print size. As a result, you may see slight errors in AF magnified many times over that would not normally be visible when the image is printed. Even if small errors in AF are visible on the computer monitor, these errors may not be visible when the image is viewed as a full size print.