Top 10 readers choice
Top 10 editors choice
Top 10 news features
Top 10 most commented on
Science magazine also has a rundown of top 2006 science and named the solving of the proof of the Poincare Conjecture as #1. The runners up are also briefly described. Obviously lots of overlap with the nature top 10s.
For those without a university subscription to Nature or Science, Discover magazine has a readers choice of top10 science news stories of 2006.
Also the Science Friday podcast (direct XML link) has a typically mediocre review of 2006 science.