If the companies are almost dead equal, I'd choose the one that supported my alma mater.
If the company that supported my alma mater totally sucked, and the other was amazing, I'd probably pick the other.
When in Ames, I felt Flying Burrito was superior to Panchero's. It had more to do with the food, but I was aware of Panchero's being from Iowa City. Maybe I prefered to give the Ames based operation my money, but at the end of day, I just like Flying Burritos better.
Down here in Des Moines, we have Bandit Burrito which just blows Panchero's (and Flying) out of the water. I haven't ate a Panchero's since I've lived here for this very reason. I have no idea if Bandit Burrito supports ISU, and I don't care because its delicious.
Now when it comes to gas stations, I can see choosing to avoid Kum & Go. Gas is gas. If you want food, QT and Casey's have better food. I stop at Kum and Gos quite a bit, but its more out of convenience. If you have a K&G, Casey's, and QT all in the same spot, K&G is my last choice.