I have both front and rear disk brakes (Shimano M475's stock on a Kona Nunu) and I've had rubbing problems on the rear brake. I thought it might be because of the amount of twisting pressure at the rear dropout and because I only hear the rubbing after hard pedaling. I agree that the rubbing is minor and the stopping power is profound but I'd still change out to rear V brakes if I only had the bosses for them (the Nunu has no rim brake bosses-- unbelievable!). I can't put a conventional rack in the rear because my disk brakes block the eyelets.

On the new bike that I'm planning I will definitely go with disk in the front, V in the rear setup. I find that I don't apply the two brakes the same way anyway so the different "feels" are ok to me. I'm going with a Rohloff Speedhub so I'll have nothing hanging around on the rear of the bike. Very clean-- and quite expensive....