Three that I actually use for commutes (ordered from most used to least used):

*Ortleib backrollers. Usually only use one unless I'm stopping for groceries.
*RELoad messenger bag. Use it days that I ride the rack-free single speed, I used to use it everyday but with the longer (22mi round trip) commute and associated crap that that brings (more clothes/etc), my back isn't thrilled hauling it everyday.
*Timbuk2 (medium). Useful for quick errands and trips that don't require much carrying capacity. Also the waterproof liner has failed in several spots (it is 10 years old.....) so only good for dry days.