I get a lot of questions regarding upgrading from SPS 2003 to MOSS 2007. So far, there has been very little information on this topic, but Joel Oleson just posted a good article on some of the upgrade options. I am intrigued by the scan option to identify customized sites/pages in a portal but I have a feeling that heavily customized sites (which most of my clients demand) are still going to be a painful process to upgrade.
On that note, if you are doing heavy customizations to site definitions and templates, it's always a good idea to warn the client up front that they will have to re-invest heavily in the upgrade when 2007 ships so they can budget accordingly. As a personal rule of of thumb I try to always present the 'doomsday' scenario as part of the upgrade discussion, meaning for every dollar the client invests today in customizations they should plan on at least a 100% matching investment to upgrade. That might be a bit over the top but personally I'd rather give them the bad news up front so they can make better decisions down the stretch.