No, I don't do it normally if there are other ways of moving a dog. However, I have recently had to lift Jesse out of deepish water because he fell in and couldn't climb out again... lifting him out by the collar would have been a lot more uncomfortable than being lifted by the (ample) scruff!
I would say it also depends on the breed. With our lurchers, I would never dream of scruffing them for anything as they just don't have enough skin for it and it would hurt them. In a situation like the one with Jesse, I would have to pull them out by the collar. Our pyrenees on the other hand has so much skin around his neck, he probably wouldn't even notice if he was scruffed...
So in a nutshell, no, I wouldn't use it as a default, but in some situations and with breeds that have lots of scruff, I wouldn't consider it cruel.
Vera