http://sheldonbrown.com/saddles.html seems relevant for seating issues.
http://www.sheldonbrown.com/pain.html is extremely relevant:
Wearing proper cycling shorts will help, but beware shorts with excessive padding, which can make it worse.
So be wary of extremely padded things. But that does only mention
excessive padding.
Your issue may in fact be your seat. Or any number of things, really, but if you're running a stock seat or one of those gushy padded seats I'd question that.