Well, I'd like to see subdual damage work like it does in PnP - that is, if you're using a bladed weapon, you take a massive hit to AB, since you're trying to hit with the flat of the blade, which is not easy, particularly after years of training in using the, well, sharp part of the sword.
To simplify, it might be more straightforward to have weapons like the sap or a billy club, or just plain old bare knuckles, do subdual damage, and leave anything else as lethal. The system from Arabel (I think that was the server name) is customizable along those lines. However, due to the fact that it requires replacement of the onDeath and onDying scripts, it might clash somewhat with the existing death system.
The other problem I can see, short of the insta-stabilize technique Penandpopper pointed out, is accidents, or "accidents". PC A and PC B are chatting out in the goblin wastelands. PC A says something about PC B's mother. PC B drops his sword and wades in with his fists. The comment was really mean, so PC B pummels the poor sap into unconsciousness. PC A is now "unconscious", with one hit point. PC B, his rage fulfilled, looks for a healing kit to patch PC A up. Meanwhilst, PC C is having a little trouble with the goblin camp. He finally makes a run for it, only to be cut down by a goblin arrow... but not before the goblins catch sight of PCs A and B. Two goblin arrows meet in PC A's body... and a fighter who eats goblins for breakfast is cut down. This is, of course, not the way it happens in PnP, but without a second way of measuring subdual damage, there's not really any way to fix that. Now, imagine you're Player B, and you have a personal grudge against Player A. How hard would it be to orchestrate just such an "accident"?
That's the biggest non-script-around exploit I can think of. I am working on a theory for an alternative, but it may be lag heavy. We'll see once I write up a proof-of-concept.
The advantage I can see to limiting subdual damage to specific weapons is that you can then limit to whom these weapons go. If some people would be irresponsible with said weapons, they don't get 'em. That's better, in my mind, than restricting things to consent-only for a fistfight.
Regardless, subdual damage is a pie-in-the-sky system... it'd be really nice to have, but there's no rush. (And frankly, I'd much rather have the ability to inflict subdual damage on NPCs than on PCs. The number of times I've wanted to knock out an NPC to incapacitate them, rather than kill them...)