Great thread! I found out the hard way (losing my favorite chickens to dogs! Fox and coons ! ARGGH) The number 1 thing we did right this time (our third coop build) is to have electricity and run two hot wires around the coop/run about 6 inches off the ground and the next wire at about 10 inches. We also dug a ditch around the perimeter and put hardware cloth into it, bent it upwards, attached it to the wire of the run/coop (livestock wire first five feet then poultry wire around the rest and doubled around the livestock wire) and then put hard red clay and gravel on top. This prevents any digging under which foxes and skunks will do night after night.
The next thing I talked DH into doing was buying me one of those carports they come set up for you. About $750 for our 18 x 22 foot one. They provide great shade and keep the rain off the run. This gave us a great area to fence in and also put the coop into so my girls just come and go in their coop whenever they like. We put down a gravel base, added LOTS of topsoil and shavings (the girls mixed them up for us nicely) and put sand in about 5 feet at one end so they can sunbathe. Everyone stays pretty dry and my d'uccles have beautiful clean feet..which is no mean feat....LOL
As far as the coop itself...my husband made ours so we can open up one whole side of it (it comes down like a ramp) and I can clean it out easily. We have a wooden floor with a rubber mat on top. Under the roosts I put large shallow rubbermaid type containers and I can pull them out, dump the poop into the wheelbarrow, sweep out anything else and within about 5 minutes everything is clean again. I don't like wire floors because poop always seems to get stuck instead of falling through. Windows are great but we also bought some of the vents you have in your heating/AC in the house and put them at the very top so we can open them up fully or if it is a really bad storm with wind, close them slightly till the morning. I second the PDZ and DE for the nestboxes. We bought a bucket with nipples and it is fantastic. The water never gets dirty, we hang it from a basket hanger and the chickens love it. It is covered and has a hole to fill from the top. No more carrying waterers that you have to flip over and get yourself wet and lose half the water and two days later they are filthy! In the dead of winter though we do have plug in dog bowls that we have to use for a time. I do not like any of the heated chicken waterers I have seen....too flimsy.
Sorry, did not mean to write a book! One day I will take photos and post them. We have 9 seramas and three d'uccle's so our coop is not as big as some. (They cannot go our free range cause we are on a busy highway on only an acre plus have roaming dogs all around us.) Good luck and have fun!