Personally, I tend to play it up regularly and especially in either extremes of the social classes. In the poorest neighborhoods, I tend to have people working in close-knit groups who are -- either by necessity or circumstance -- not only wary of strangers, but also of what is visibly different than they. This extends not only to racial considerations, but, say, obvious cybernetics or magic, etc. In the richest parts of the city, I tend to have the people populating them to be rather discriminatory against any person whom would not fit in by style, appearance and general manner (again, it sometimes extends to cybernetics -- though the magically-active are less likely to be shunned, it would likely be the case for, say, a Rat Shaman and the like).
I find it adds personality to the different social strata, and helps give the persons peopling the different districts a bit of a more distinctive personality (even if it could feasibly border upon stereotypical views and plausibly take away some of that personality in favor of generalization).
It's my belief that Shadowrun is a very fine setting within which to explore social tension (and cultural discrimination) and I must admit I enjoy injecting it into the game, if only to make it feel more believable.
