I use an improved version of Complete Divine's mechanics.
[sblock]
Destruction of the Undead.
Instead of making undead run and cower, turn attempts deal positive energy damage to all undead within a 30ft radius burst of the cleric. Turning undead is a standard action that deals 1d6 damage/cleric level to all undead within a 30ft radius burst of the cleric. The affected undead get a Will save (DC 10 + Cleric level + Cha mod) for half damage.
Evil clerics (or any cleric that can swap out spells for inflict spells) still Rebuke Undead as explained in the PHB. Paladins work just as you would expect, they turn undead as a cleric three levels lower.
Undead with turn resistance now treat that ability as Damage Reduction vs turning damage, at a rate of 2.5 per point of turning resistance. Thus, your average vampire with turn resistance of 4 would essentially have DR 10/- vs turning damage.
When this ability is used against incorporeal creatures, you do not have to roll a 50% miss chance; turning hits them automatically.
Under this variant system, a greater turning works like an empowered spell. After rolling turning damage, multiply the result by 1.5.
Under this system, a character with 5 ranks of Knowledge (Religion) increases the save DC vs his turn undead attempt by +1 (Clerics rebuking undead still gain a +2 bonus to their turning damage as per PHB).
Additionally, some turning feats work differently under this system.
Disciple of the Sun: You may spend one additional turn attempt to perform a greater turning.
Exalted Turning: Raise your effective cleric level by three for turning effects (+3d6 dmg, +3 DC)
Quicken Turning: You may spend one additional turn attempt to turn undead as a swift action. You may still make only one turning attempt per round.
Widen Turning: This feat replaces Empower Turning (Complete Divine). You may spend one additional turn attempt to double your turn radius.
The effects of Disciple of the Sun, Quicken Turning, and Widen Turning stack.[/sblock]
edit: with this variant in place, any "positive energy dmg" now goes up against TR. Undead needed a boost anyways.