My colleage Inma and I have been wrassling with the SharePoint web site metrics recently. You guessed it - it’s the Out of the Box site reporting that you get, well, out of the box with MOSS.
J&J also uses WebTrends - and we have an account, but we have discovered some odd discrepancies between WebTrends and SharePoint data. Our Portal was also not originally coded to “work” with Web Trends - so while the pages now contain the Web Trends tracking code required, it is still difficult to use WebTrends reporting to report on a site-by-site basis across the site collections.