I can't think of anything more likely to cause guild drama than the loot rules the guild implements. Strict systems of DKP can lead to DKP hording, meaning that people who could potentially be gearing themselves up and helping the raid more choose to have a potential upgrade sharded because they're after a 'better upgrade'. Lax systems which don't use DKP can lead to coveted items going to someone who is just lucky, rather than to someone who is recognised as deserving it.
Which system is better? I think it depends on the instance and on the group of people you have at your side. If you're in a friendly, helpful, unselfish guild that is raiding ten-man content then rolling could well be your best bet as the group you are in will likely be able to see past their own wants to the guild needs and let the person who needs the loot most have it.
If you're in a large guild of drama llamas raiding 25 man content then you probably need a solid DKP system to stop people bleating about the unfair allocation of loot to new people, or whatever they're about to bleat about. With a strictly defined system of loot allocation there is little room for people being unaware of who a given piece is going to, should it happen to drop.
Is there a middle point though? Can you have a DKP system without DKP hording? Can you have a roll based system where people are rewarded for the effort they put into progression runs? It's almost impossible to design a system that will work for every single guild, because the drama llamas in one guild might be mighty beasts, able to make drama out of something others see as perfectly fair and reasonable.
In Coup de Grace we have a very loose set of raid loot rules. Primary specs can roll for an item, but if you win an item you're expected to set aside your right to roll on the next item. You don't have to, you can roll, but if you are rolling against someone deemed to be in greater need of the item then your roll may be ignored. If no primary specs want the item then the off-specs get to roll. If no off-specs want it then it gets sharded and the shards put in the guild bank. It has served us well so far, some runs yeild loot like water for one class which is the way things go some times. Other runs only serve to boost the prowess of our off-spec abilities. But most people are happy to pass over their priority if it means gearing someone else up who needs it.
We've been considering implementing a DKP system for our progression into Gruul, but it's hard to know how this will change the dynamic of the guild. Will people suddenly start to feel entitled to items, even if they can't really make use of them? Will our newbies start to get shafted, only ever getting the detritus no one else wants? It's really difficult to know what is for the best.