FWIW, here's my setup for a fairly short (2-mile) commute:

1984 Peugeot P8 road bike with Nitto moustache handlebars and Suntour bar-end shifters. Drop bars don't really make sense in urban traffic; I find MTB-style bars really uncomfortable. Moustache bars give you a choice of several hand positions.

I know a lot of people swear by the Brooks saddle, but I'd rather have a plastic one (I've got at Terry Cité Y) that won't get soaked in the rain.

I've got Wald folding baskets on the rear rack. Yes, they're heavy, but I find it easiest just to throw my regular briefcase into them, rather than trying to squeeze it into a pannier. They also make it easy to do my shopping -- I've just got a bunch of canvas shopping bags. When it rains, I just shove my stuff into a trash bag.

Right now I've got Zéfal half fenders, but I'd like to get full fenders. I use the Performance store-brand Kevlar tires. Kool-Stop salmon brake pads make a big difference.

Definitely, definitely wear a high-visibility reflective vest at night. Even in the daytime. The cheap ones you can buy at Walmart (or similar) in the work-safety department are actually a little more convenient than the ones designed for biking, 'cause they're made of very thin material and can be folded up really small to fit in your pocket or bag. I also use rechargeable batteries for the lights.

I don't take tools or supplies with me -- just a cell phone. In the event of a breakdown on the road, I'd usually rather just call a cab (or a friend) to get me and the bike home (or lock up the bike and come back for it with my car). Or just walk, if I've got time. Much easier to work on the bike in my basement than out on the street.