The advantage of using Google webmaster tools is that you notice early when Google encounters a problem with your site, SY
Yes Google webmasters tool is good option. you can use http://www.google.com/websiteoptimizer to optimize your site.
I am using Google Webmaster Tools for analyzing the data when I am optimizing the site only for Google. But for other search engines I use different tools like an add-on in firefox - Quirk SearchStatus, then there is website grader, alexa, compete and so on.
Google webmasters is a good options but it is good if you also consider other reliable sources like compete ,Alexa etc .