Like many have said, it depends on your commute. You probably want your travel to be Safe, Reliable, Enjoyable. I mostly cary stuff others have mentioned.
One thing I keep in my bike bag is bus fare. Haven't needed it yet, but it's always there. I also have a pencil and a couple of note cards. Pencils tend to last better than most types of pen.
About 9 miles each way. Rarely, maybe never more than twice per week.