Beyond buying a fancier domestic lugged frame (which I'll never be able to afford), I don't think I need to make another upgrade to my commuter, it's finally perfect. I just gave her a bath so I grabbed some snapshots. The only change I'd make is some 170mm cranks, but the 175s are fine and I don't do any high cadence riding on this baby anyhow. The most recent upgrades are the front hub and light system, and the tubus logo rack. Both were absurdly expensive, but worth every penny. This bike started as a stock Cross Check Complete two years ago.

Upgrades:
48mm Nitto Noodle bars
Cane Creek Gummy levers, Nashbar Cross levers
Nashbar short stem
Lumotec IQ Fly Senso Plus with B&M tail w standlight
Peter White front wheel w Nexus generator hub (disc compatible for future)
Woody's Fenders
Schwalbe Marathon Supremes 700x40c (rear tire has a Mr Tuffy for insurance due to Nexus hub)
Brooks Champion Flier Special Edition
Tubus Logo Rack
Hebie Chainglider
Nexus 8 Premium hub Rear Wheel from Continental Cyclery
Velo Orange Leather bar tape over Fitzik gel pads
Acorn Small Saddle Bag (old style)
Velo Orange Bell
Boulevard Smokestack Cork bar end plug