I judge a station by a couple factors.
1. General cleanliness and condition of pumps, nozzles, visible filters etc.
2. How my truck runs on it after a tank or 3.
3. How many pumps are Diesel vs gas and who fills up there.
4. Price and convienance.
I like a medium sized station that is clean and has a few fleet accounts to keep turn over short ( but doesn't have to be a truck stop). A biggie is how clean the pump, nozzle, ground, hose, and any filters are. Big truck stop are good usually but most big truck company drivers are not necessarily diesel enthusiast and buy where told or is right off highway. I too have had a major truck stop right off the highway with lots of big truck customers have poor performance (mine was a Pilot). It was a drivability smoothness issue not stalling though.
The difference I believe comes from tank, filter, and distributor maintenance. Most fuel is regional but there can be a significant difference in turn over and fuel bulk tank "polishing" and maintenance. Turn over is not quite as important as filter and tank maintenance to me (within reason).
Look over at Power Service website for a little info on bulk tank maintenance additives and "polishing".
You can get a slug of crap fuel from a tank that has not been "polished" in a long time and running low with lots of disturbance from many others filling up just as easy. I have filled up at a decent sized Exxon truck stop right off the highway and picked up water (water in fuel light).
I have seen pump service techs working once or twice but haven't gotten a chance to talk to one yet but I bet they could tell you a lot.