I use a simple perl script to filter out autloaded requests (.css .js .gif etc), internal requests, and worms (there are so many these days), and then dump the whole log into a SQL database.
This provides *the best* analysis tool there is. Virtually every question I've seen here can be answered with a simple SQL query. (I use mod_usertrack to keep track of users in between sessions). Want to know which referer refered the most users who come back more than three times? Simple query. Which page caused users to visit the Contact Us page the most? Simple query. And, if you don't know SQL, you can just a GUI'd db like Access which does it for you.