I've just checked what Mr Google says about this ... engine cooling seems to be the consensus as to why run-ups should be done into wind.
http://4vfr.com/?goto=view_article&s...rticle_key=118
http://www.oaafly-in.com/oaawebsite85e/11ACPOM.htm
http://www.ufly.com/lessons/ground_operations.html
BTW, at 'busy' airfeilds without designated run-up bays, where's the best place to do the run-ups?