Besides Google Analytics, which is probably one of the best in the market currently, another notable one which has received good reviews would be
103bees - Search engine traffic analysis and statistics tool. I run both GA and 103bees on my site. Recently, the latter has also added spot question search queries into the program that allows you to know what visitors searched for that led them to your site. This allows you to write targeted posts as you know what your visitors are searching for.
Hope this helps.