I'm certainly a fan of a rack/panniers or even just a big trunk bag rather than a backpack. I commuted for a few weeks with a few different backpacks (different sizes) and nothing felt good. They had two problems for me:

1. Sweaty back ... there's no getting around this one no matter how much a backpack claims to let your back "breathe"
2. Center of gravity. The heavier my bag, the more unstable I felt on the bike on descents (and I have a big one each way on my commute).