I use many log analysis programs, depending on the need.
As an ISP, we run Webtrends Log Analyzer for the basic hosting.
As an SEO company, we are moving our marketing clients to NetTracker for an advanced hosting/analysis solution. In addition, for marketing clients, we typically use a combination of NetTracker and ClickTracks.
There are a lot of smaller, faster programs out there, but to get one to do everything is fairly difficult. Besides, I've found that multiple views of the log are a good thing. Each program can show you a different aspect depending on the philosophy of the person that created the program.
'Course, there is always reading the raw log data - that's always fun
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