Hi Chris,
Over the years I've tried many web log analysis tools both commercial and free and in my opinion the best thing available now is the free Google Analytics service. You just add a script they provide to the bottom of your skin just before the closing body tag and it starts capturing, the next day you can start seeing data in the reports they provide. Its really awesome. Microsoft is coming out with a similar poduct called Project Gatineau but it is currently invitation only. I requested an invite several months back and haven't heard from them yet but google analytics is available today.
Other tools do log analysis whereas google tracks actual pages as they are viewed. I also download my log files and and process them with a free tool, awstats, but I find it exaggerates traffic due to all the bot and crawler traffic.
Todd Lewis has also done some work using Webalizer. He has a technique for parsing the logs from a multi site mojoportal installation so you can see traffic reports of the individual sites. He started some documentation on this here: http://www.mojoportal.com/multisiteweblogtricks.aspx
Of course google analytics also works fine for multi site installations since the script goes in a site specific skin.
Hope it helps,
Joe