When I was there, the Stanford EE department flunked about half the students taking quals, but the physics and (especially) Applied Physics quals weren't as ugly. At the time I thought EE was profoundly disrespectful of the students, but on reflection I changed my mind. If you flunk your quals you're on a Masters track, and a masters in EE is a highly useful professional qualification, whereas in physics it isn't.
Applied Physics did its weeding out on the front end--in my year there were a grand total of twelve of us admitted--but took a lot of care that everybody graduated unless they screwed up badly. Since I had a wife and daughter by the time I took my quals, that was very comforting. :)
Cheers
Phil Hobbs