Fenders are your friend. Fenders will protect your feet and back from a spray of dirt and water on wet days.
Panniers or Messenger-style bag? Panniers attached to rear (or front) rack and can carry a lot of gear, such as your work clothes or foul weather gear. Or, if you prefer not to use a rack, consider a messenger style bag or a backpack. Just remember, weight on your back is weight on your butt!
Carry the right tools. Equip your saddle bag with a set of tire levers, a multi-tool, a spare tube and a patch kit (since lightning DOES strike twice on occasion). Tuck in a pair of surgical gloves too - it will keep dirt and grease off your hands during that flat tire change. Don't forget the pump!
Practice changing your tires on the living room floor once or twice. It will build your confidence for the day when you'll need to do it on the side of the road.
Vary your route occasionally. Try to choose lower traffic routes that will be pleasurable, not stressful.
Lighten your load. If you dislike carrying your work clothes, or they need to be pressed/ironed, consider driving to work occasionally to leave a few clean changes of clothes and pick up the dirty.
Dress appropriately. It's best to start out a little cool, as you'll quickly warm up once you get moving. In cold weather, consider warm gloves, a skull cap or headband to keep ears warm and toasty, and a jacket to protect you from wind and water.
Be visible! Reflective bits on your clothes, shoes and bike will make you more visible to drivers. Red blinking tail-lights and white front head-lights can be seen from quite a distance and can alert drivers to your presence more quickly.
Put eyes in the back of your head. Try a helmet- or eyeglass-mounted mirror such as the Take-a-Look mirror. After a week of knowing preceisely what's approaching from the rear without having to turn your head, you'll wonder how you ever got by without one.
Ask your employer about bike-to-work incentives. Some companies have cash rewards or other incentives for employees who bike to work.