My colleague Phil Schewe at AIP has now revealed his pick for physics story of the year, as well as his long list of runner-ups. Several of the Physics News Update items in the list (the ones on dark energy, the new WMAP data, wireless energy transfer, and stock market criticality) were stories I wrote up.
Coming up soon at sciencewriter.org: my own picks of the top 10 science (not just physics) stories of 2006. They will be up at the end of next week.