Factory mod is easy, the Speedmaster forward controls, those count as factory don't they? If not then the short rear fender/multifunctions.
After market, is a tougher decision.. To date, I suppose the air box delete wins out over the California mini apes, because most of that was done with raw materials, my own tools and hands.
This category may change in the near (I hope) future, when my Alex Leather craft one off custom seat arrives.
Honorable mention HAS to go to my Powercommander V, because,, you know, MORE POWER!!