Tracking user navigation methods by logging where users click on web pages

I wrote about some research we're doing in my organization to observe user interaction with navigation by tracking where users click on the page (body, local navigation, breadcrumbs, global navigation). Our observations aren't dissimilar to what Michael Bernard observes in usability testing -- links to content are most often searched for/clicked in the body of pages. Navigating our site (a digital library) consists mainly of browsing through a directory (a-z lists are available as are a poly-hierarchical directory listing), so what we were mainly interested in was how people made use of the links in the local navigation. I'd be interested in seeing if other people have done this and what they were looking for. I find, as an in-house site developer, that being responsible for a site for a long term (as opposed to just launching one and going on to a new project) gives one good opportunity to observe and assess the site for usability. Your can assess patterns of use over long periods of time. You can make contact with users and keep the lines of feedback open with them over time. Clearly there is something unique about being involved in the evolution of a singular site, which I am only beginning to appreciate.