There's not much discussion on this subject as yet, but Stone Temple recently ran a basic analysis between a few different stats programs:
http://www.stonetemple.com/articles/...may-2007.shtml
Unfortunately, they simply compare how they measure traffic more than anything, rather than the individual plus & minus points of each application.
However, I'm sure we'll see more in this arena soon.
Meanwhile, I'm hoping to start something with IndexTools this week...