Bike:
Keep in mind your goals. If this is a commute-only bike, get something that can meet all your commute needs. If the bike is for more than commuting (mountain biking? road riding?), make sure it will can meet your commuting needs as well. Can it accomodate fenders and a rack, i.e. does it have the braze-ons? Is there space on the handlebar for lights? Will you be comfortable for the X number of miles you have on your commute? I also use a cyclocross bike, set up as a commuter with a rack and panniers, to be able to run wider tires on a sturdy but road-geometry frame. A touring frame could also meet these needs, and would leave plenty of room for panniers.

Rack and Panniers
I've seen three general methods for carrying gear mentioned here: rack and panniers/trunk, backpack, and messenger bag. The main advantage of panniers/trunk is the gear is on the bike, not on you, and it can't pull you off balance. The disadvantage seems to be that it has to be taken on and off, and requires fitting a rack to your bike. Some people like the extra space panniers provide, while other like the aerodynamics of the trunk. Backpacks don't require any attachment, and are useful for other things. But they cover your entire back, which can make you hot, and if you have a lot of stuff, can make you unstable. They also add a number of extra pounds on your back, which can be uncomfortable. Messenger bags sling across one shoulder, and have some of the advantages/disadvantages of backpacks. I find them to be less disruptive of my balance than backpacks, though, and come with pockets for my bike stuff.
I use panniers and a messenger bag to carry a laptop. In my panniers, I put my work clothes (I leave shoes at work) on one side, and my lunch and water on the side. I also carry my wallet, keys, cell in a one pannier pocket, and my bike repair stuff and Kryponite chain-and-circle-lock in another pocket.

Repair Kit:
Two spare tubes
Patch kit (redundant, but it's happened!)
Tire levers
Pump
Multitool
15mm wrench
Money for the bus
Back up batteries

Lighting:
Get a lot of light up front and back. Steady and blinking in back, and something that will help you see as well as be seen up front. There are lots of systems out there, and many past discussions here on the board regarding HID vs. halogen vs. LED, rechargable vs. battery, brand vs. brand. Make use of the search feature on the boards to learn more. Good lighting isn't cheap, though sales always help, but ignoring lighting may make you less likely to bike, as you won't feel as safe as you could, and it will make you less safe.
I use a two light (12 watt/20 watt) headlight, relying mainly on the 12 watt for regular weather early morning commutes, and both for dark nights and rain. It is a rechargable system. I use the Cateye LD-1000 on the back, set for half solid, half blink. I don't have a back up for my front lights, but I should.

Routine:
I pack the night before, getting everything in the panniers and making/packing my lunch.
In the morning, I shower, eat breakfast, put the lunch in the panniers, put the panniers on the bike, and set up the lighting. I leave early, between 5:30 and 6:30, which helps to beat traffic and give me some cool down time before work. I don't shower at work in the winter, but do in the summer, and the extra time comes in handy. I wear light, polypro clothes, not necessarily bike specific, but light (and layered for warmth in winter) so that I don't overheat. At work, if I don't shower, I wash my face and give myself time for the sweat to dry. Then I change. After work, I try to wash my cycling clothes regularly, so as to be too stinky when I have to do something after work in my cycling clothes. Mainly, I try to stick to a routine that works for me, as I find it helps eliminate the chance for me to find excuses to not bike in.