I used a backpack for my first 2 years commuting. It affects your balance, you sweat under it, and you are limited as to what you can carry.
I now have Ortlieb panniers, and i can set things in them ( liquids, for example) and when i get to my destination, they're right where I put them. I can balance my two panniers on my bike so that it doesn't affect my balance at all. And i don't get that sweaty back or sudden shifts in movement like i used to get from my backpack.