This is the finished product! - I have a watering nipple system in the closest left corner of the run in this pic now. I have a 2 gallon bucket hanging with a pvc pipe coming out of the top so I can just stick the hose in and fill it up!
I made the run detachable... I figure if I want to move it or have issues this is the easiest way to get inside of anything

I filled the inside here with sand! Pine shavings in the nesting boxes (there are 4 nesting boxes on the left). I ran a board across the bottom of where the door meets the floor of the coop (not in this pic) so the sand would stay inside.

This shows the boxes better. Sorry about the mess! Was putting the walls up this day. I framed it in my garage and finished it outside. The boxes are 1 foot wide by 1 foot tall by 1 foot deep. That seemed to be everyone's consensus online of the best size.

I let them out with the door on the bottom. The big door is for cleaning.

I loved all the ideas so I thought it best to give this site some props. I never found a real plan so I just winged it as I went. All in all i'm happy with how it turned out. Our 3 hens are happy. :)

The coop inside is about 4x4 feet plus 1 foot nesting boxes. The coop is about 27 inches off the ground and has an 8 foot run counting the 4 feet of under coop area. This was built mid summer of 2013 a good hour south of Atlanta GA

- Edit - Now it's almost the end of summer 2014 and everything has changed! We went from 3 hens to 17 birds! Here's how I made it work -
Our coop - we went from 4 chickens to 17! I had to take our original smaller coop (yellow one) and attach a bigger one to it (blue one). I made a pass through door to connect them and expanded the run a ton! I have 9 gallons of water available with chicken nipples and two two gallon bucket gravity feeders underneath for feed. Sand inside the coop works great!