Well, here is a method of peeling a pomegranate that eliminates almost all the mess, and a method of juicing them for use in recipes (or drinking straight, which is another tasty option!).
Step 1: Ingredients
> a sharp knife
> your largest mixing bowl
> very cold water
You will need (for juicing):
> a large zipper style plastic bag
> your pomegranate arils
> rolling pin or something heavy-ish
> something to keep your bag from slipping as you smoosh it (optional but nice!)
> a strainer of some sort
> a small bowl to catch the juice
For both, it is handy to have a damp paper towel at the ready. Pomegranate goes from awesome to dang-it-a-stain very fast if you are not prepared!
Step 2: Slice and Score
Once you have the top off, score the sides 6-8 times from your cut around to the bottom. You don't need to go too deep.
Be sure to clean up any juice off your counter right away to avoid stains. If you get it on your clothes, I have had good luck soaking fabric in cold water and oxyclean per the package directions (got it off some white aida cloth I was embroidering on without running the color in my embroider floss ... though it is better to just not get it on your clothes if you can help it!)
Step 3: Soak
Now, soak your pomegranate for around half an hour if you have time. You can certainly work on peeling it right away in the water, but soaking it will help soften the rind and make it easier to handle, which is especially helpful if you've been storing your pomegranate for awhile (I've had this one about 2 weeks).
Step 4: Peel
Working gently, loosen the top edge of the rind away from the arils. This may be difficult at first but it really gets easier as you get going, because you have more room to work around the fruit.
If you find the center bit is too hard to work with, you can carefully slice the top of it off. I found this made it much easier to loosen the arils and split the pomegranate into chunks. Chunks are easier to work with than the whole fruit!
As you work, you'll see the other awesome benefit of peeling under water: the arils sink and most of the rind floats!
Step 5: Remove the Rind
Step 6: Bag It Up
Put the arils in a good zipper type plastic bag and squeeze out most of the air before you seal it. You don't need to get all the air out, but you don't want to be fighting a big air bubble either.
Step 7: Smoosh It!
I find that it is best to work mainly from the outside in. If you work from center out you end up pushing seeds into the edges of the bag and it stretches. You don't want to break the side of the bag open!
Work gently and apply firm steady pressure as you go. When you start hearing the seeds snapping, stop. Too many cracked seeds can affect the flavor of your juice!
Step 8: Strain It and You Are Done!
First, open your bag and roll the zipper part down. This is not strictly necessary, but does help stop you from flinging juice around since the seeds will come out without catching on the zipper.
Put your strainer over your bowl and carefully pour your seeds and juice into the strainer. Use your hand or a large spoon (like a gravy spoon if you have one, or a serving spoon) and gently press the arils into the strainer to release any remaining juice. Stir them around and repeat once or twice until you are satisfied you have got it. Again, be careful not to snap/crack too many seeds so you don't affect the flavor of your juice.
Voila! You have just peeled and juiced a pomegranate!