My left femur is 1/2" shorter than my right... errrr... I mean my right femur is 1/2" longer than my left ... noticeable if I tell you about it and stand without shoes, but not as noticeable w/ shoes on (I wear a 1/2" lift inside my left shoe).

There is nothing I've been able to do to compensate for the difference except set my saddle height to a good spot for my right leg, then lower it every so slightly to compensate for the left - so the saddle height is actually off on each side by about 1/4". My right knee takes more stress from this, so I wear a patella brace on it, which has helped relieve any on the bike pain from the setup. My left pedal stroke is much, much smoother than my right no matter how I set it up.

Luckily though I've never had any pain caused by this issue. Cycling actually relieves all lower back pain that I've had due to my f'd up skeleton.