For me, commuting, backpack. That's because I stop in the morning at a McDs at a bad location. I've come out several times and found someone going over my bicycle. Even though it is parked where I can watch it thru the window as I stand in line.
Of course you could carry your panniers around with you. I prefer to leave them on the bike myself. Each of us will have good reasons for doing the commute "our" way. You have to see what works best for you.