We've spent the past four days doing user acceptance and regression testing on our branding, and I've found a couple of essential additions. Expect more as the testing wraps up over the next week or two:
Also, I wanted to emphasize the near-inevitability of the need to customize the LAYOUTS components. There is no escape... ;) Here's a far-from-complete list of a few high-visibility components in the LAYOUTS directory that the most common role used in collaboration sites (Members) will have access to:
Take a few minutes to see what Visitors have access to and you'll get a smaller list, but enough to cause a jarring user experience if you've done anything more than modify the theme. And don't forget this big one... If you're deploying personal sites - everybody's a site collection admin and sees all the LAYOUTS pages.