On my road bike, backpack. I only commute on it a few months of the year in dry, warm conditions. I carry very little on those commutes.

The rest of the year, rack and panniers on my touring bike. Way more comfortable than a backpack and the capacity to carry a lot more gear (clothing, layers, raingear.)

It depends on the type of bike, the level of comfort you want, the amount of gear, and how much you are willing to spend.

Oh, and this probably the first thread to discuss this subject, right?