Well, FWIW, here's how I do it.
First, let me say that I have a 100 gal farm-type transfer tank on my truck. I fuel at truckstops (since I run OTR) for 3 reasons 1) fresh fuel, 2) high volume pumps (remember, I'm pumping 130 gallons here) and 3) I can get in there with my 40' trailer in tow.
When I buy the "big tank" of fuel, (100-130 gal) I tend to shut down, since I am checking the oil and draining the seperator at the same time. in the amount of time I'm going to be there, I can safely check the oil w/o a chance of overfilling or worrying that it's low.
When some 300 miles down the road I'm transferring from the in-bed tank to the truck tank, I leave it idling. In fact, other than fueling, my engine typically doesn't stop from the time I leave the house on a run until I return. My reasoning is simple: I live in the truck with a dog. Sleeping in the truck, I don't want windows down (even cracked--there's been a rash of ether attacks in truckstops lately) -- so I use the ac/heat. when I'm not in the truck, the dog needs climate control too, and I'm not about to leave the truck with a window open and me not there--so it all goes without saying. When we shut down at Motel 6 for a stretch in a real bed, I shut the truck down.
Does this hurt the engine? Well, time will tell--but I've put 52,000 miles, and 1900 hours on the truck since I bought it on labor day 2003. Oil analysis on 15,000 mile oil shows no significant soot build up, and my analysis reports show that I could run the oil even longer. At this point the truck uses "0" oil between my 15,000 mile oil changes, and gets me a total calculated avarage of 14. 6 MPG (as calculated on my federal fuel tax forms).
I'm not saying idle the truck for the sake of idling, but if you want to for 15-20 min while you grab a big-mac, no problem, and if you feel the need to idle for 8-10 hours while you sleep all night, don't sweat it. After an entire night of idling, I do see some smoke for the first 2-3 miles, but it blows off.
Just sharing my personal experiences. Your mileage may vary.
--Chris