I am looking to remove all my sites from Analytics and even webmaster. Piwik seems reasonable. I used Piwik on single domain and really loved the real time reporting. I will look into cross domain management, something like single dashboard for multiple domains. Currently want to switch about 40 WordPress sites to Piwik. Will also look at clicky though.
The OP might have been asking something different though. I think he/she wanted to find out keywords his/her site ranks for. Webmaster tools would show SE traffic queries from impressions and rank while software like traffic travis and services like Web Grader from Hubshout, webCEO, woorank might do the same. I am not 100% positive.
It would be Great (hint $$$) to have software/service which simply allows you to enter a domain and returns all keywords the domain ranks for. Not just the keywords you manually add than "track rank" or ones that currently get impressions for searches.
I am sure many would pay for the service , like per query or small monthly fee etc. (Hint, Hint programmers $$!!)
anyways, good luck