-Forget PUGs. I know, you've heard this before, but if you really want your instance runs to go well, pick up groups just aren't going to do it, period. Get yourself a guild (make sure it's not a "pickup guild"-- a quick test is to see if they have a website and forums), and it'll make instance runs much, much easier and more fun. If you have to have a PUG, try to stick to friends and people you've grouped with before. Random LFG is more like "looking for trouble."
-Study up. There are guides, maps, and strategy all over the place for every instance in the game (yes, even RFC). Look at them. Know the routes, know the mobs, know the quests-- where to go and what to do. Not only will it help the group go smoother, but it'll help you with looting, too. Things are much more fun when you know what loot to hope for-- and you get it.
-Have a leader. If you've done the studying, it's probably you, but the best way to make sure an instance goes well is to choose one person to lead and have everyone follow them. One person chooses a route, one person assigns targets, and one person calls pulls. Organization is the key (which is usually why PUGs don't work).
-Prepare! The boy scouts were right: Repair before you go into an instance. Get together to share quests and buff. Make water and food, make healthstones when needed, keep an eye on soulstones, shaman bring ankhs, locks bring shards, and hunters bring arrows.
-Be patient. There's a lot of reasons to get frustrated in instance runs: wiping, not getting the loot you want, people making mistakes, people leaving early. Don't let it get to you. If you do a few instance runs and things go south, go solo for a few levels, come back, and it might make all the difference in the world. Instances, especially high lore stuff like Maraudon, Scarlet Monastery, and the Sunken Temple can be some of the most fun parts of the game. Have fun in there, and don't fret the small stuff.
Instances can be tough, but when you're in there with a great group and you know what you're doing, they're definitely worth it. Following these tips will help you do just that.