I don't think one should get too OCD about it...my SS has two different wheels, rear is a Hope SS hub. But both are nice wheels of simillar quality and appearance. I don't think I'd be happy riding a bike with completely odd looking wheels, though.
I know exactly what you mean by the way. I get anxious when my valve caps don't match the colour of my bike.
But this was covered in a poll a while ago.
Why should rims match? The rear wheel is under more than twice as much load. The front wheel is dishless.
Have you noticed how much more common it is for a back wheel to be buckled?
If I ever get a bike that I decide I want to keep forever, it'll have 32/36 spoking. It would have 40 hole spoking on the back wheel if I could get rims like that.