No hard-and-fast rules for commuting clothing versus what you might wear when on a "regular" road ride. The key to your outfit is flexibility. Obviously, weather conditions can change between your morning and evening commutes. So you'll want a bike wardrobe that promises maximum versatility. For me, that would entail two or three light layers during cool weathera synthetic T-shirt, long-sleeve jersey made of a wicking, fast-drying material such as the REI Power Dry Zip-T ($38), and some kind of water-repellent shell (Performance has a great buy on its Gore-Tex jacketjust $199 for a cycling-specific raincoat). If your commute is less than an hour, then I don't think you need a really serious Gore-Tex rainsuit. Lighter materials will work fine, as you can dry them during the day even if they soak through a little.
During the summer months, of course, you can get by with much less. Baggy shorts might be more comfortable and airy than skin-tight ones; something like the Pearl Izumi Mesa Bike Shorts ($75) would work. I'd wear a regular bike jersey, though, as these not only wick well but the bright colors and back pockets will keep you safer, while providing a place to store an en-route snack.
Additionally, invest in a good headlight system so you can keep up your commuting in the winter. At a minimum, get a 15-watt system such as the Planet Bike Insight ($150), a very affordable headlight with three power settings that allow about three hours of run-time. If you can swing it, though, look into one of the new generation of turbo lights, such as the NiteRider BlowTorch ($409) or the Light & Motion ARC (also around $400, depending on the mount). They're expensive, yes, but they put out an amazing amount of light, equal to 30 watts, and have single-charge run-times of close to four hours.
Not many changes needed for the bike. Maybe a luggage rack, or buy a courier-style bag for hauling your stuff, like the Ortlieb Zip-City Medium ($86). Fenders, definitely. Flats would be a hassle, so install tire liners or treat the tubes with Slime, a useful tire sealant.
Gear checklist: REI Tech Tee; Performance Gore-Tex cycling jacket; Pearl Izumi Mesa Bike Short; Planet Bike Insight; NiteRider BlowTorch; Ortlieb Zip-City; Slime.