I've tried different hops for bittering and am convinced that there is a difference in flavor. To me it seems like after being boiled for 50 minutes (or whatever), the aroma and flavor from the hop oils is gone. But there is something else. I don't know the science behind it, but it's different. As Bob357 said, there is a difference in smooth or harsh, but there's something else, too. For instance, in a Nut Brown or Hefeweizen, it seems that the bittering hops really contribute to the overall flavor.
JMO