I got my 2013 Jamis Commuter 1 CmX second hand with less than 60 miles on it from someone who overestimated the Nexus 3's hill-climbing ability, and was surprised to find that it didn't really need a lot of optimizing; never-the-less, here's the list:

• Original wheels were scrapped for beefier Mavic A319 rims with DT Swiss spokes, Shimano LX front hub and the original Nexus 3 in the rear.
• Stock v-brakes where below par and were exchanged for Avid Single Digit-3 and recently for Shimano Deore units and Shimano cables.
• Light weight alloy rear rack and Brand-X 25 liter panniers.
• Magicshine 808 was modified with wide-beam lens, better battery pack and custom installed on the fork above the front mud-guard paired with Blackburn Flea 2.0 (flashing) on handlebar.
• Spanninga rear-rack light (steady) and PDW Danger Zone clone in flashing mode on seat post.
• Airzound during the coldest and hottest months of the year (when car windows are rolled up).