Resale, it hurts. Riding, it doesn't. I'm very seriously considering a 9-sp Ultegra group on a Cinelli-branded Centurion. To a non-bike person, it will look just as good, it will definitely ride better, but in my mind: clash. I think there are more than will admit that run Shimano on Italian bikes, and Cilo had no problem loading up it's Columbus frames with Dura Ace and 600.

Other than the brand situtaion, why not run your best group on your best frame?

And if you went to a couple sites right now, you could order a Cinelli frame and build it with Dura Ace or Ultegra. No problem there.