It seems that as javascript page-tagging becomes the more popular choice as a way of processing web stats, there's not as much work being done on log-based analysis tools anymore in the marketplace. My office used to use a product called LiveStats.XSP. It wasn't the greatest tool by any means, but it did have some nice features. It was recently bought by Microsoft and is no longer supported however. It abandoned log analysis turned into a proposed Google Analytics killer called Microsoft Gatineau, which supposedly is good at determining the demographics of your visitors, including age and gender (yeah sure...)
When I was looking for log analysis software a while ago, I wanted to avoid anything that looked overly bloated and enterprisey, which is what most stuff seemed to be, focusing more on the marketing and advertising aspects of reports.
One thing you may want to look at is the new version of Urchin, Urchin6 (see features here). Urchin I believe was bought by Google a few years ago. It's offered as a locally installed solution, and with it you have the option to use either page-tagging or log file analysis for any site that it monitors. There also seems to be some interface ties between Google's own web-based Google Analytics and Urchin. It's not free though, unfortunately, and I think you can only get it through authorized partners.
It does all the standard logfile analysis stuff, everything is browser-based, the reports it offers are pretty deep and comprehensive, and it also seems to have a few bells and whistles that other services don't offer. For example, I remember it being able to present a view of a web page it tracks with colored hot spots overlayed on top of it, based on how often users click on items on that area of the page. Worth checking out the demo of it anyways.
