I use 'visitors' ( http://www.hping.org/visitors/ ), which was written by my friend, YC.news visitor antirez. I tried Google Analytics too, but found it kind of annoying in that it's sort of a pain to get the information I want.
Thanks David, note that in most debian-based distributions all you need is apt-get install visitors. Edit: Also if you could like to play with real-time analysis to get detailed information about how your users are interacting with your web site please feel free to write me at antirez -at- gmail ~dot~ com for a free invitation for http://lloogg.com
I used it from 2004-2005 for clicktrails... great idea and implementation. Graphviz makes everything better (corollary: anything that needs Graphviz is interesting enough to get better)
Google Analytics and/or Visitors are about all I would think a person needs. And now that you have lloogg.com out there, it looks like clicktrails are covered in a GA-style interface. Kick ass! Great idea, again, best of luck.
I haven't run into many websites that couldn't be improved by clickpath analysis and refocusing navigation on the ways people actually use a site -- optimizing for the common case, in other words. It baffles me that any site would fail to do so. Now they really have no excuse.