Selected answers from the Dumb SEO Questions Facebook & G+ community.
Per Jacobsen: Google Analytics with +Justin Cutroni s modification of the tracking script as described here: http://cutroni.com/blog/2013/01/14/a-new-method-to-track-keyword-ranking-using-google-analytics/ - otherwise there are lots of services out there like Moz, Searchmetrics, Serps.com etc.. Do you need an online service or downloadable software?
W.E Jonk: http://piwik.org/ is an opensource alternative to GA.