I recommend carrying spare inner tubes. Fold one on itself, wrap it with a rubber band and put it in a ziplock bag with a little talcum powder. It's much quicker to put in a new tube than to search for, find and patch a hole on the roadside, especially if it's raining, getting dark or you're short on time. The "weight penalty" is small. I carry two tubes, but then I cover some glass-strewn roads in my city. I carry an old Tyvek envelope strips to use as a tire boot.

I agree about lights to see the road and also to make you more easily seen. If you have a white handlebar- or helmet-mounted light (or even a Photon light), you'll appreciate it when you have to make low-light, roadside repairs.

Plenty of good bicycle commuting sites online. See Paul Dorn's, e.g., at http://www.runmuki.com/commute/

I like MDinana's suggestion to take spare set of clothes/shoes to leave at work if possible.

Personally, I carry water and bags on the bicycle rather than on my back (gets too hot), but some prefer backpacks and Camelbaks. I use an old Carradice saddlebag to carry a few tools/tubes, rain jacket, lock, Clif bar. Oh, and my bike has fenders.