IMC, clerics no longer turn undead by default. I set up a system called divine channeling, similar to what Khaalis mentioned, but different. Basically, all clerics start with a number of channeling attempts equal to 3 + Cha mod. The types of channels they recieve depends on the Domains they select. For example:
Animal Domain: Master of Beasts- by expending a turning attempt, the cleric can turn/rebuke/command animals. This is handled exactly like a normal turning attempt. At 10th level, the cleric can affect magical beasts as well, although they are treated as 10 HD higher than their actual HD.
Destruction Domain: Weaken Object- by expending one channeling attempt, the cleric causes one object he touches to lose a number of points of hardness equal to twice his level for 5 minutes per cleric level. Magic items receive a save (DC 10 + 1/2 cleric level).
Evil Domain: Turn Good- the cleric may expend one channeling attempt to turn good outsiders, undead, fey, sprits, or divine creatures (including priests and paladins of good deities). The turning attempt is handled identically to an undead turning attempt.
Healing Domain: Divine Health- by spending a channeling attempt, the cleric or one he touches becomes immune to poison, disease, and ability score loss for a number of rounds equal to 3 + the cleric’s Wisdom modifier.
Luck Domain: Divine Fortune- by expending one channeling attempt, the cleric can reroll one roll that he has just made. You must take the reroll, even if it is worse than the original roll.
Magic Domain: Metamagic Master- by expending a number of channeling attempts equal to the metamagic feat desired, the cleric can infuse a spell he currently has prepared with ANY metamagic feat. The cleric doesn’t have to know the metamagic feat, although if he does, it takes up one less channeling attempt to use (minimum 1 channeling attempt).
Protection Domain: Divine Resilience- by expending a channeling attempt, the cleric gains a DR equal to his Wisdom modifier for a number of rounds equal to ½ his cleric level.
Travel Domain: Evasive Movement- by expending a channeling attempt, the cleric may move through opponent’s threatened areas without suffering attacks of opportunity for a number of rounds equal to his Wisdom modifier.
War Domain: Battle Mind– by expending a channeling attempt, the cleric may enter into an altered state of intense battle focus , gaining a +2 bonus to Str, +2 Con, and +1 AC for a number of rounds equal to 3 + his Wisdom modifier.
These are just a few of the channeling abilities I came up with. There are around 60 domains in my game, each with its own channel. I have been using these for about two years now, and so far they have been extremely useful to all characters who possessed them, but not overpowering. It also goes a long way towards keeping all clerics from being carbon copies of each other (a big problem in 3E and 3.5).