Effects Refer To Limb Loss, With No Mechanic
There are many references scattered throughout the rules to creatures regrowing severed limbs and severed body parts reverting to their original form. Yet there are almost no rules covering how it could happen in the first place.
There are no 'called shot' rules within Official D&D 3.5 rules, and the damage rules are intentionally abstracted. The closest are the Variant Rules for Damage to Specific Areas on p27 of the 3.5 DMG.
Making the game 'grittier' by making limb-loss and death by beheading possible is not necessarily a good thing, but called shots as optional rules existed in AD&D 2e definitely, and it had the Sword of Sharpness, for example; on high rolls it severed parts.
Untested House Rule: Extrapolate From the Hydra, Giant Squid and Kraken Rules
The hydra's combat rules are fairly complete as to how sunder works against them:
To sever a head, an opponent must make a successful sunder attempt with a slashing weapon.
This is not unreasonable, in fact it's pretty good, but ruining a limb might be reasonably accomplished with a bludgeoning weapon, and the sundering rules for objects, which both kraken and squid reference unchanged, supports this. The limitation to slashing is likely a holdover from 3rd ed., where sunder required slashing only (PHB 3.0, p136, 'Strike a Weapon'). This DM doesn't see piercing weapons as reasonably disabling limbs.
(The player should declare where the attack is aimed before making the attack roll.) Making a sunder attempt provokes an attack of opportunity unless the foe has the Improved Sunder feat.
This is the 'cost' of the 'called shot' option; take an AoO or take a feat. The would-be sunderer still has to succeed an opposed attack roll, modified by creature size and weapon size. Natural attacks are usually 'light' weapons, but this DM would rule that for this check they're 'one-handed', and heads are '2-handed', just to keep things cleaner.
An opponent can strike at a hydra’s heads from any position in which he could strike at the hydra itself, because the hydra’s head writhe and whip about in combat.
This is a holdover from the facing rules of 3rd edition, and barring Unearthed Arcana options, can be ignored; you can attack any part of a creature, and it can attack in any direction in D&D 3.5.
An opponent can ready an action to attempt to sunder a hydra’s head when the creature bites at him.
You can do this with sunder versus a held weapon as well.
- Each of a hydra’s heads has hit points equal to the creature’s full normal hit point total, divided by its original number of heads.
- kraken’s tentacles have 20 hit points, and its arms have 10 hit points.
- giant squid’s tentacles have 10 hit points each.
This is the part that differs with the rules-legal sunderable natural weapons or heads; the HP calculation.
This DM would probably rule that the Hydra's head-HP rule should be the basis for all heads; full normal HP divided by original number of heads.
Alternatively, rather than the explicit rule, you could extrapolate that since hydras have 1 HD/head, then each creature's head has 1 Racial Hit Die plus Con modifier per head. Therefore fey have weaker necks (1d4+con) than undead (only vampires, mostly) (1d12) or dragons (1d12+con). The benefit, if it could be said to be, is that it's a static number; humanoids will always have 3.5+con HP per head. It makes Vorpal weapons hugely overpriced; just get sundering (MIC p.44) as a +1 add-on.
Limbs are more difficult to adjudicate, but allowing only the sundering of natural weapons, other than bite (heads) rather than limbs simplifies things. If that is done, primary weapons would have HP as light weapons of the creature's size, and secondary weapons would have HP as light weapons of one size below the creature's size. This appears to be how the kraken and squid tentacles and arms are priced.
Fine-Tiny: [Weapons either too small to target, or treat as 1 hp ea.]
Sml: Pro, 1 hp; Sec, [untargetable, or 1 hp]
Med: Pri, 2.5 hp; Sec, 1 hp
Lrg: Pri, 5 hp; Sec, 2.5 hp
Hug: Pri, 10 hp; Sec, 5 hp
Grg: Pri, 20 hp; Sec, 10 hp
Col: Pri, 30 hp; Sec, 20 hp
Weapons that would have less than 1 hp are either too small to sunder, or they merely have 1hp minimum, DM's choice.
Losing [an attack or head] deals damage to the body equal to half the [part’s] full normal hit points. [Losing all of its heads kills living creatures that have heads]
This is good as-is, for the most part.
The Game Would Change
Intelligent creatures, as well as many unintelligent predators, would use this method in melee, especially if the lower value for head HP were in use. It's effectively what feline predators try to do in real life; sever the spinal cord near the prey's head.
Living creatures with heads, and all creatures with natural attacks would become more vulnerable, but allowing melee attackers to 'disarm' (Ow, the pun! It's excruciating!) creatures' natural attacks gives non-spellcasters 'save-or-die' and 'debuff' options without long feat chains.
That's verisimilitude, sorta.