It depends on the effect you want.

If you want a natural view, the separation between the images should be about 6.5 cm/2.5 inches, equal to the distance between the average person's eyes. However, if you do this, the stereo effect is limited to relatively nearby objects (6.5 m/20 feet), and objects that are too close will give a "double vision" effect rather than a stereo effect.

If you want a scale-independent view, you should adjust the separation based on the distance to the subject. A good rule of thumb is that the separation should be around 1/30 the distance to the subject. This lets you create stereograms of things like mountains.

Separation is largely independent of focal length, though you need to be careful about using telephoto lenses when producing stereograms: if the foreground or background shifts too much between the pictures, a person viewing it cannot combine the two images into a single view.

The technique I use is to take three images: the second image has a separation from the first that seems right for the subject, while the third image is separated from the second by about half as far. This gives a "separation bracketing" effect: I can use whichever of 1-2, 1-3, or 2-3 gives the best appearance. Note that I'm usually hand-holding and judging distance by feel; if you're using a tripod and measuring everything out, you may not need to bracket.