Use clip only when it is necessary. Keep in mind that there are cases where clip isn't necessary such as rendering opaque geometry. Typically this leads to two permutations of the pixel shader, one with clip and another one without.
Clip may save pixels from being written to the screen buffer, but on the other hand, it may have detrimental effect on the z-buffering optimizations. So, if you absolutely need clip, call it as early as possible in the pixel shader.