El Coke pretty much hits the nail on the head. Personally, I prefer the C&TS for several reasons: As El Coke notes, the scenery along the C&TS (excepting that bunch of cabins and crap around Los Pinos) is about as unspoiled as you will find anywhere in Colorado or northern New Mexico. The crews, as El Coke notes, have mostly been with the railroad for a long time. They are a great bunch of folks. And, the LACK in Chama or Antonito of all the tourist-trap garbage found in Durango is actually a plus for me.
The biggest disappointment of the D&S is not under the control of the railroad. It's the out-of-control growth in Durango and the Animas Valley north of town. That has really changed the character of the train experience for those of us who remember Durango in the 1960's and 1970's. Where the D&S redeems itself is from Rockwood to Silverton. The Animas canyon is one of the prettiest in Colorado--and, unlike virtually every other major river canyon in the state, it doesn't have a highway next to it. I excuse the D&S for their more "restrictive" attitudes about what passengers can and can't do on the train, and for having the yard closed off to casual visitors. Handling the number of passengers they do in a typical day makes that necessary and I accept that as a price of success for the railroad.
Bottom line: they are both great train rides, both among the best anywhere. And, in a time where such historical attractions seem to be falling into greater and greater disfavor among a population increasingly uninterested in such things, both railroads need people who will patronize them.