Really depends on your climate, your set up (roof? no roof?), your run management, etc. More information about those things can help narrow your choices down. The most popular choices are probably sand and deep litter, but they work very differently from one another.
My runs have semi-deep litter(cold composting), never clean anything out, just add smaller dry materials on occasion, add larger wood chippings as needed.
My in-town setup had one more chicken in it than really ought to have been there but I never had an odor problem that couldn't be solved with a few more inches of shavings, straw, pine straw, fall leaves, etc.
I cleaned it out a couple times a year when it got too deep and started spilling through the wire.
I really like my sand floor because it is so easy to rake out the food they didnt want, and the poos as well. I rake then shovel into a bucket and it goes into the compost. I hardly ever have to top it up with fresh sand. I have also found that the sand floor makes it easier to see bits of rubbish you don't want them eating, and never would have thought could be there. I think the deep litter method would be more fun for them, but I let mine out as much as possible, so I'm happy with that.
I have too many predators to let them roam too freely, so they spend a lot of time in the run. It is good size run, and I am curious what I should use as the flooring? The run is about a year old now, and is all dirt. Some spots are getting worn, etc. I have a tin roof so it stays pretty dry in there unless there is a windy rain storm. Any suggestions of flooring are appreciated.
I use deep litter (mostly leaf/stick gathered from the trees surrounding the cleared portion of the pasture) and what straw is either kicked from the box or made from ripping out/cutting down tall weeds in the pasture, on top of dirt. Well, technically, its clay sands and sandy clays - dirt would drain better.
One of the first things I did, after fencing the run, was carefully observe rainwater runoff following a heavy storm, and regrade portions of it to take advantage of natural tendencies in the terrain.