An Introduction to Log File Analysis for SEOs & Webmasters from Eric Lander is a must read for all SEOs out there. He says that if you are not looking at your raw log files, you are missing out on things, even if you have the best web analytics software. Eric goes through the various key metrics in the log files that are key in your log file analysis process.
A Sphinn thread has extremely positive discussion around the article. I wish I had more time this morning to share my thoughts, but the article is great and the discussion makes it even better.
Forum discussion at Sphinn.