"The expression rule of thumb has been recorded since 1692 and probably wasn’t new then. It meant then what it means now — some method or procedure that comes from practice or experience, without any formal basis. Some have tried to link it with brewing; in the days before thermometers, brewers were said to have gauged the temperature of the fermenting liquor with the thumb ... This seems unlikely, as the thumb is not that sensitive and the range of temperatures for fermentation between too cool and too warm is quite small. It is much more likely that it comes from the ancient use of bits of the body to make measurements. There were once many of these: the unit of the foot comes from pacing out dimensions; the distance from the tip of the nose to the outstretched fingers is about one yard; horse heights are still measured in hands (the width of the palm and closed thumb, now fixed at four inches); and so on. "
World Wide Words: Rule of thumb