Over the year, I have commuted from 20+ to 10 miles RT, and lately I have shifted from a typical road bike to something much more like a self contained touring rig (LHT, 38mm tires, front and rear racks). I carry about the same as others who have posted - my tools, spare tube, and patch kit reside in an under seat bag, and the clothes, toiletries, and chow go in panniers, front or rear as the load requires. I have found that I like to leave the panniers on the bike. Therefore I pack up my cargo in thin nylon sacks which I can easily remove from the panniers - this also helps keep the contents dry. One thing I always carry is a small first aid kit. It ia nor used routinely, but when it is needed, it is needed.
I think those who have pointed out the need for flexibility and versatility are absolutely correct. The one thing that apparently hasn't been mentioned is the need for superior visibility. Even if you don't wish to, sooner or later you will be riding in the rain, snow, and or dark. I would emphasize side reflectors, brilliant, if not gaudy paint jobs, spoke lights, and anything else that would make the bike commuter more obvious. I commute with two headlamps, one on my handlebars and one on my helmet. This winter I will be increasing my side and rear visibility.
I disagee with many here about the need for fenders. My experience is that road splash from passing cars gets me far wetter than the stuff thrown up by my tires, but my racks block some of the tire fluid. More and more, I tend not to ride when it is wet anyway.
I think reliability is a key system component for a commuting rig. While I can fix some of the more common problems, I would far rather not. Hence, my affection for 38mm tires and overbuilt rear wheels (40 spokes with Phil hubs)