I use a hit location system for my Spycraft campaign. Basically, armour has no bonus to defence, but acts as damage reduction only (obviously only certain hit locations - jackets covering chest and abdomen, helmets covering head etc). Hit Location is a single D10 roll. Each body part has individual hit points assigned to it (typically characters will get 1-2 HP per level per body part - so in total they have much more HP than a normal Spycraft character, but any given body part is much more vulnerable to multiple hits).
Area affect weapons will either be divided across the entire body (or those parts not behind cover), or else assigned to 3 hit locations. For example, a fireball from an explosion will be divided across all 10 hit locations. Whilst damage from a frag grenade is divided in 3, and each location (possibly the same location more than once) gets 1/3 of the damage.
Recovery is based on HP per hit location per hour - unless the character is wounded (if any hit location has all available hit points used, then any further damage comes off the central wound pool).
Cover no longer affects defense, but instead offers additional armour protection and possible concealment. So if an enemy is standing behind a crate, any hit which is behind the crate is actually a miss (unless its a potential threat, in which case its assumed the round hit the crate at the correct point to vector onto the target hit location). Should a potential threat occur, then the crate provides damage reduction.
(Much of this is borrowed from Twilight 2000 and Traveller 2300 hit location rules)
The end result is a little more (perceived) realism, a lot more anxiety in individual fire fights, and yet a quick recovery rate between action scenes. Given the combat oriented nature of our Spycraft campaign, we've found it works really well.
Spycraft has the advantage over DnD in this area that virtually all the combatants (apart from the occassional guard dog) are humanoid, and so use a single hit location chart.
You may want to check out the following:
Star Wars Galactic Campaign Guide - simple hit location chart, with location-specific affects for called shots
Torn Asunder - detailed critical hits for DnD, covering non-humanoid creatures as well.