That is a very good question, Anthony. Loot distribution rules can be a very tricky thing to handle when you bring a PuG into the mix.

If you happen to run a loot council system, then you can usually get away with retaining that form of loot distribution. LC is what my, now formally, guild used and throughout our Naxx days when we were struggling to get members, we continued to use it even when he had PuGs in the raid. There were a few cases where the players were not comfortable with trusting us, but every run that where we did use it went perfectly smooth without any loot disputes at all. You just have to make sure that your council is being as fair as possible when giving stuff out. People will get upset if you are clearly only going to be giving all of the best stuff to your own members, but so long as you spread the wealth around, there should never be any problems.

DKP is little harder to deal with. In the case of a DKP based guild, you many want to consider switching to being LC run when running with PuGs or just using an open roll system. A possible solution is to give each PuG member an aggregate amount of DKP based around the average amount that your current players have and follow your loot rules as normal. Say that you usually spend 5 - 20 DKP per item and your raid's average is around 35 DKP. You 'gift' 35 DKP to each PuG that they can then use to bid on items as they want them as they would if they were a normal member of your guild. It would probably be much more difficult to get PuGs to buy into using this method, but it could work.

As mentioned, you can also just go with open rolls, but that can usually cause some of your personal raid members to get a bit upset about things, especially if not everyone is on the same level in respects to loot.