I used to work overnight shift. What you wear or what lighting you use is going to vary.

1st, How long is your commute? If it is less than an hour some cheap flashlights from dealextreme should work fine. Something like the Ultrafire WF-502B should work well. Don't forget you will also need batteries, charger, and bicycle mount. You can get all of them from there as well. Just expect about 2 weeks for delivery.

If your commute is longer than an hour then the Magicshine lights are usually highly recommended.

For tail lights the Radbot 1000 and New Super Flash turbo are recommended. A reflective vest is also a good investment.

However, being visible is great in most situations, but not all. There were parts of my commute were I would ninja and occasionally salmon it. Some places you might want to just blend in.