Rather than giving a flat stat reduction, I would apply situational penalties (losing a leg shouldn't give a dex penalty for fine manipulation tasks).
For an arm, I'd probably start of with a -5 to most balance type activities and combat, scaling down to no penalty after the character became accustomed to the situation.
For a leg, there are obvious affects on movement, although with a prosthetic limb I could see a character getting back up to 1/2 or even 2/3 movement eventually. Perhapas no running though.
Eyes (ok, they're not limbs), penalties to spot and missile fire.
For a head I'd go with a large, permanent Con penalty.