Get some good Lake or Chrome commuting shoes. Lake at one point made this awesome set of shoes called the I/O Boa's. Probably the best set of commuting shoes I ever owned. Sadly they are no longer produced.

Now I would say go with a set of Chrome shoes, a little pricey, but well made, comfortable, 2 hole pattern. Match them up with some Time ATAC pedals and your good. (Time ATACs are what all my courier friends used, I took a set of Crank Brothers with me on Tour and while they are nice the cleats wore down and I had a few accidental unclips during my ascent of the Col du Gran Colombier, not fun, my friends who are couriers SWEAR by ATACs and have gone so far as to say that they will not use any clipless system other then that when they ride fixies because it is the only one that they have never had accidentally unclip)