I bike to work every day and I have been doing it for the past 10 years.
So from experience:
Spare inner tubes. You wanna try to find a puncture in the dark, by the light of a torch, in the rain? Be my guest....
Patch kit. Fix the punctured tube at work/home.
Brake cable.
Spare links for the chain. If the chain breaks, your in D.S.
Small adjustable wrench.
Bike Multitool.
Head torch.
Pump. Get a decent quality one.
Wear a reflective vest. If you have a bag, make sure it's a nice bright colour. Cammo is a no-no. Put a reflective band around it. You cannot be too conspicuous.
There are tyres on the market that are puncture proof. I use the "Armadillo" brand. High density rubber with a Kevlar inlay. They guarantee no punctures for one year. My experience seems to bear that out.

When you set out in the morning, take your time. Give yourself time to warm up. Use your gears. Look around. Be aware. Assume that every other D.H. ON THE ROAD'S MISSION IN LIFE IS TO TURN YOU INTO A ROAD KILL! Everyone else on the road has a safety cage wrapped round them. You don't. Any hint of trouble, get your ass up onto the sidewalk.
Other than that, enjoy yourself. I do.