It is a very subjective thing, many people swear by messenger bags other only use panniers.

Personally I switched from backpacks to panniers for commuting recently. Panniers are more comfortable, less sweaty and have a larger capacity than a backpack.

When I commute to school I actually put a backpack in one of my panniers to make things easier when I get to where I'm going.

As a Washingtonian we get a lot of rain so having a weather proof set of panniers is also a big plus as my Northface Recon let water in.