Our dogs have pea gravel arround the trees/shurbs in thier dog run. Then over the grass we put rubber stall mats from UFA. It works great in the winter, as you can shovel it right off (I put the smooth side up)
It can get a bit slippery in the rain, but they dont run arround to much in there.
The do run is right out our back door, so it has a walk way in it that is concrete as well.
For odour, we clean and hose out our run every coupple of months. In the winter we just shovel the snow arround the trees and allow them to "potty" on the stall mats.
We use ProTect (industrial kennel cleaner you can purchase from Kane Vet Supplies or some smaller private pet shops on special order) about 3 times a year. Its pretty toxic stuff, but it works great. (DO NOT MIX IT WITH BLEACH OR A CONTAINER THAT HAD BLEACH WATER IN IT!!! =Smoke bomb that burns your lungs)
Then every coupple of months during the spring/summer/fall we use a concentrated mixture of Odourmute. It seems to be working like a hot D*mn. You really have to saturate the area, but it does work.
I would try to stay away from mulch etc as it attracts bugs, and if your dog run is close to your house, it will encourage bugs to come in during the winter. If you want a good "masking" smell, put some cedar bark chips in a large pail or barrel (tall enough so they cant pee ON the bark chips) Keep it in a dry spot (under a tree or something) and just stir it up every coupple of days or so, and your dog run will smell so good you will want to hang out in there!
haha - okay, maybe not THAT good....