All the advice so far has been great. Now I'll add my 2 cents.
My commute is ~9 miles one way.
My old commuter was an aluminum frame road bike with a Delta seatpost mounted rack and panniers. It was ok but not the best. My new commuter is a steel frame cyclocross bike. The frame material and geometry provide a more enjoyable ride on the crappy streets of Atlanta. The frame has all the braze-ons for "properly" mounting a rear rack.
I never was able to convince myself that it was worth the extra cost to buy waterproof panniers (yes, I'm cheap - sometimes) so never ride to work if its raining. If its raining on the ride home that's ok. I don't mind getting home with wet clothes but arriving at work with soaked clothes isn't my idea of a fun day. Just in case I keep an extra pair of socks, slip-over shirt, pants, and sneakers in my desk. We dress casually where I work. Shorts in the summer.
My old commuter had SPD pedals (Shimano M-535) which I thought were pretty good for making a fast getaway in traffic. My new commuter has Egg Beater pedals. I rate the SPDs at about an 8 and the Egg Beaters get a 9.5.
I like the drop handlebars on my cyclocross commuter. They're just like my weekend road bike. I'm not comfortable on a mountain bike.
My old road bike commuter had caliper brakes and when I had to stop in a hurry, especially on wet roads (remember the panniers and rack add a lot of extra weight) it got kinda scary. My new commuter has cantilever brakes and stopping is much more predictable.
My old commuter would not accomodate fenders, other than SKS RaceBlades. They were held on with zip ties and would sometimes shift sideways and rub the tire. My new commuter has lots of clearance for regular bolt-on type fenders. I haven't installed any yet, but.....
I have always liked lots of lights. I want to be seen. I have the reflector that came with the bike and the reflectors in the spokes. Looks kinda dorky but its something else for motorists to see in the dark.
I have two blinkies on the back of the rack and two more that I can clip to my panniers for side-mounted running lights if its raining or foggy.
I have two NiteRider headlights and a 3-LED flashing white light.
http://home.mindspring.com/~rhorne/Jamis%20004.jpg
I have lots of reflective tape on the frame for added visibility.
http://home.mindspring.com/~rhorne/Jamis%20015.jpg
I always wear a hi-viz yellow-green windbreaker or vest. In the warmer months I wear bright yellow or hi-viz jerseys.
I carry everything I need in my panniers - clothes, wallet, lunch, snacks, work papers, money (coins) for phone calls (no cell phone), cable lock, PowerGel (just in case), spare batteries for the blinkies, band-aid, etc. In my seat pack are the usual bike tools, spare tube, and patch kit. I have a mini-pump attached to the seat tube.
If it "might" rain for the ride home I have rain pants and jacket and shoe covers. In the warmer months I ditch the rain pants and shoe covers.
Hope this helps. Did I cover everything?