I started doing mud runs in 2010. I've done multiple mud runs every year since, most of the big names (haven't done Foam Fest or Rugged Maniacs yet) and some small local ones.
I have gotten scrapes at plenty of the mud runs I have done, but that's always been from the rocks in the mud pits. That one with glass and trash in the mud sounds disgusting, and fortunately, I have never see that myself. Believe me, if I did, I would never go back there.
Most of the mud runs do seem to go through growing pains, so I don't know if I would do the very first mud run someone local is putting on, but after two or three, they will quickly be learning from any mistakes. Honestly, some of the small local ones are my favorites. They can be more creative and less crowded.
Tough Mudder is tough. I did it once, and that was enough for me. I can say I did it, but I enjoy the ones that are 5K much more. I still do Camp Pendleton each year, which is a 10K, but that's about it for me length wise.
Here's another secret. I rarely do the burpee penalty. I'm out there to have fun and cross the finish line. I do try the obstacles, and if I can't do it for some reason, I just move on. I'm not competitive, and I know I never will be. I do them late in the day after the winners have been determined. I just have fun.
General advice for any mud run:
Training: Run. Or at least walk. Yes, you can walk the entire course on race day if you want, I see people doing it all the time. If your point is to get moving and cross the finish line, speed doesn't matter at all. Do keep in mind that you will have running breaks for obstacles. In fact, you might even have to wait in line for one or two. The more distance you can cover in your training the better, obviously, but remember on race day those breaks are coming.
Obstacles: You will have to climb over stuff (small and large walls, hay bales). There will probably be a balance obstacle (I so wish my balance were better). There are often monkey bars. There might be some others, but they are pretty much a variation on those basics. If you are lucky, you'll get a slide of some kind as well. Of course, there are the mud pits. How many will depend on the race. Some you will just walk through, but at least one you will have to crawl through so you can get good and muddy. It's why you are out there, right?
What to wear: Do not wear anything you remotely care about. Assume everything you wear will be sacrificed to the mud gods. Having said that, I do find I can wash most of the mud out of things - or at least make it look like that - after a couple of trips through the wash after rinsing it out at the venue and again with an outdoor facet when I get home. Still, I have my mud run clothes (including shoes) that I just wear for mud runs.
As a general rule, you don't want to wear things that will absorb water because they will get heavy. Also, pockets will tend to collect mud. Generally, I wear old running shoes (I really need to replace my mud run shoes), non-cotton (or low cotton) socks (most places sell moisture wicking running socks, including Wal-Mart, which is what I'm talking about), compression shorts under nylon type shorts (I was wearing board shorts for a while), and a white cotton T-shirt. (I know, I know, that last one goes again everything I said, but I like to have something that shows how muddy I got. It slowly turns tan despite my washing and then I replace.)
Clean up: All good mud runs have a way for you to clean up afterward. Usually, it is group showers outside. No matter how much mud I think I've gotten off, I still find plenty more to get off when I get home, but this cleans you up enough to get home without getting your car muddy. They should also have changing tents so bring a change of clothes. You will want a plastic bag to put your muddy clothes in for the drive home.
That's everything I can think of right now. Hope it wasn't too long and rambling for you. By all means, sign up for one. As you can tell, I love them, and they are great motivation to get you outside exercising.
If you have any more questions of specific question, please let me know.