I prefer pdfs with the margin always on the left. Printing two-sided pages at home is a pain. Usually, I just print out all the pages and put them in a 3-ring binder.
I prefer pdfs with the margin always on one side, since most of the time if I print a pdf I either staple it together or (rarely) put it in some sort of binder. And I'm used to it that way... reading pdfs that have alternating margins somehow grates of my nerves. It seems like a bad layout to me.