Over at gleemax, I made an undead subtype that used d8 HD and they had a Con score. This was reserved for undead creatures with a metabolism. Still, I see that as more of a house-rule at this point than something I want to hash out in a balancing project. Personally I don't see much issue with the d12 undead HD.
The only problem I've seen with the undead HD (including its 1/2 BAB advancement) is that melee undead creatures need a rediculous number of HD to be effective, rendering level-appropriate turning moot. Part of the revised turning rules I created in the Combat & Rules thread help to deal with this. So, even if you can't turn them with the PHB mechanic, you can still damage them.
Robby, if turning does damage, what does rebuking do?
In short, rebuking heals undead and hurts living creatures. Note that I renamed it to Bolster (as that's really what you're doing at that point). There is an improved version of turn and bolster available as a feat. The improved turning is what dazes undead creatures on a failed Will save. The improved bolster (called rebuke) controls undead on a failed Will save (with certain limitations). The full version of the mechanics are in the spoiler below:
[spoiler]
Turn UndeadI wanted to make a slightly less clunky mechanic. This is a slightly modified version Bier posted (possibly from Piazo?)
Turn UndeadYou create a burst of positive energy centered on yourself with a thirty foot radius. All undead creatures in the area take 1d6 points of damage per Cleric level. All living creatures in the area are healed for half that amount. You are not affected by your own turn attempts.
Undead creatures with Turn Resistance take less damage. For each point of turn resistance, reduce the number of damage dice by one. So if a ninth level Cleric (9d6 turn damage normally) would turn a vampire (turn resistance 4), he would roll 4d6 damage less, so he would only deal 5d6 damage to the vampire.
Bolster Undead (replace rebuke undead)You create a burst of negative energy centered on yourself with a thirty foot radius. All undead creatures in the area are healed 1d6 points of damage per Cleric level. All living creatures in the area take damage equal to half that amount. Living creatures may make a Will save for half damage (DC 10 + 1/2 Cleric level + Cha mod). You are not affected by your own bolster attempts.
Improved Turn UndeadPrerequisite: Ability to turn undead
Benifit: When you turn undead, all undead creatures in the area must make a Will save (DC 10 + 1/2 Cleric level + Cha mod) or be dazed for a number of rounds equal to half your Cleric level plus your Cha mod.
Rebuke UndeadPrerequisite: Ability to bolster undead
Benifit: When you bolster undead, all undead creatures in the area must make a Will save (DC 10 + 1/2 Cleric level + Cha mod) or risk falling under your control. If your Cleric level is at least double the undead creature's hit dice and it fails its Will save, it is under your mental control. You may control any number of undead creature's whose total hit dice does not exceed your Cleric level.[/spoiler]