This is my big problem. I use one of those TransIt garment bag panniers (it looks just like a mini-garment bag, and drapes over the rack.) I kind of like the pockets for organizing and such, but it's heavy (when loaded with my clothes, lunch, shower materials, and the usual bike-emergency stuff, it's about 13 pounds), it's not waterproof, and attaching the bungee hooks is a minor pain in the neck. It also somewhat obscures my rear taillight. I have a very nice set of Ortlieb panniers, each of which is *much* lighter than the garment bag, attaches and de-taches with zero effort, and is waterproof. (I think the "big bag" approach might bug me for commuting, though.)

I only need one pannier to hold my commuting stuff, but I've tried it, just tooling around the neighborhood, and I hated the way the bike felt. Maybe I just need to give it more of a chance and I'd get used to it. Or maybe I'd end up with a giant left quad and a puny right quad.