The Surly Cross Check may just be the perfect commuting bike. It has attachment points and braze-ons for any conceivable configuration, and is at home as a simple fixed gear as it is a fast club rider, light tourer or commuter, is made of steel so will last forever, and is affordable as either a frameset or complete bike. The semi horizontal dropouts and "Gnot-rite" spacing mean you can run whatever drive train you can envision, and the downtube braze-ons let you run old school friction shifters if your heart desires (mine does). I've used mine as a fast club rider, light tourer, and obviously, tons of commuting. I've had it loaded it up with all manner of stuff, and no matter what I throw at it, the bike rides well, and takes an absolute beating. Add in the ability to run some heinously large tires, with fenders, and you've got a true dream machine.
Mine has gone through a few iterations, but the current set up is by far my favorite, and perfect for commuting on DC streets. I've got some Schwalbe Big Apple tires, which are massive pieces of rubber and push the frame clearance to the absolute max. They soak up all the bumps and cracks in the road, transforming the bike into almost a full suspension commuter. Velo Orange racks and fenders provide splash protection and let me carry all my junk with panache. For simplicity, I went with a 1x9 setup, with downtube friction shifting, which means no shifting adjustments. The Nitto Albastache bars put me in a nice, upright position for comfort, and the Velocity Dyad rims, laced to XT hubs give me a bombproof wheelset that will last forever. For my derrier, the venerable Brooks B-17 sits atop a Velo Orange Grand-Cru seatpost for a one last touch of comfort and class. This set up gives me the ultimate in comfort and utility, and I absolutely love it.
For more build details, including fitting the Big Apples into the Cross Check frame, check out Scott's website here.