I started commuting wearing khakis, running shoes, and a t-shirt. Once the weather warmed up I switched to cycling shorts, but kept the t-shirt. That's how I commuted all summer. Now that it is cooling off a bit, I've gone back to the khakis, but find them uncomfortable on my commuter. On my roadie, I'd never ride in anything but shorts, cleats, jersey, gloves, glasses, and everything else roadies usually wear.
I'm thinking of getting some padded tights, or some other type of full length cycling pants to use for the occasional commute.