Plan ahead and over prepare
If you know that you're going to be short on numbers for a particular raid, jump on things early and try to start seeking out more before your planned start time. It's good to get guild members in the habit of signing up for a raid or at least letting you know when there's a scheduling conflict and they can't attend. That way you're not sitting around delaying the raid in the hopes that more will log in. If you know what numbers you'll have in advance, you can start advertising for more an hour or more before your start time, and hopefully you'll have those gaps filled without delaying the raid.
Being able to invite guests in advance of the start time also gives you a window of time to brief them on planned targets, loot rules, and important instructions. The more you're able to prepare a guest in advance, the less time you'll waste during the raid trying to get everyone on the same page.
Your guild might have its own set of rules that works well, but if you're including guests, you might need to go with something different. If the bulk of your force is made up of guildies, you could probably stick with what you normally use, but if it's mostly non-members attending, it's wiser to go with something that gives everyone an equal chance at loot. Also, consider the value of the guests who are there. A guest who's the 20th DPSer might not be as key as a guest who's in the number one heal role.
One system that would be perfect for a PUG raid is the gold bidding system. Essentially, players would bid on loot with gold, and the person who bids the most wins. Meanwhile, the gold is collected and then split up at the end of the raid, and everyone who attends gets an equal share. In short, gold becomes DKP. This system is great for PUG raids because it eliminates the debate over whether someone should get priority on a particular drop (like mains vs. alts, guildies vs. non-guildies, etc.). And it encourages players to join because everyone walks away with something even if he doesn't get a piece of loot. People tend to shy away from PUGs (for good reason), but this loot system makes it much more tempting to give it a try.
Repeat, repeat, repeat
Your guild might be so well-coordinated that you can get everyone on the same page with just a quick command. But PUGs have many more unknowns, so it's essential to repeat important instructions and key information as much as possible. You don't know if Bob the healer was making popcorn when you went over the loot rules or Sally the tank was chatting with a friend as you explained the strategy for a fight. You also can't assume that everyone actually understood the way you phrased something, so make sure to encourage people to speak up if they aren't clear on what to do. Try to make use of both voice chat and text chat as well and even macro some of the most important information so you can fire it off more than once.
Your way might not be understood
Guilds tend to come up with all sorts of unique ways to approach a fight, and while it's great to see guilds tackle a problem and solve it in their own way, it also means guests might not be familiar with how you do it. For the guest, your guild might feel a bit like Seinfeld's bizarro world, where things seem familiar but slightly different and not always easy to understand. Any time you have someone along who has not raided with you before, you have to go through things as if you're doing it for the first time. And the more first-timers you have with you, the clearer you need to be. That extra minute or two that it takes to explain things and follow up with questions is worth it because the alternative might be a wipe and a redo, which will take a lot longer.
Patience is scarce
PUG raids generally fall apart faster than a guild raid would, partially because there's not as much of a sense of loyalty and partially because PUG raids can be more chaotic, disorganized, and overall miserable. So if you do run a PUG raid, try to establish a fixed stopping point ahead of time. That way, someone who might be ready to bail on your call for "one more try" might stick around knowing that there's only 10-15 minutes left before the raid is done for the night. Also, you can't really get away with banging your head on things the way you might if it was just a guild raid. If you're on try number four or five, you might want to either call it or move on to something else, or you'll risk people suddenly realizing they have to go mow the lawn and wash their car (yes, at 10 p.m., so what?)
PUG raids can be a little trickier to run, but if the leader pays attention to detail and communicates well, things can run smoothly. The two biggest reasons for PUG failures are poor organization and lack of leadership. But if you are an assertive leader and can clearly explain instructions and strategy, there's a good chance of success and a fun night for all.
Do you have a guild problem that you just can't seem to resolve? Have a guild issue that you'd like to discuss? Every week, Karen Bryan takes on reader questions about guild management right here in The Guild Counsel column. She'll offer advice, give practical tips, and even provide a shoulder to lean on for those who are taking up the challenging task of running a guild.