Have you found that having a really organized Root Page is helpful? At first I didn't think it was because I figured users would be coming in from the SE's to specific areas.. but now I'm rethinking that.
Home page is a navigation tool, but its also a critical sales tool. Home page helps to push sales of products that are linked from the home page. I track sales by adding a?hp to the end the URL which is then passed on to my shopping cart.
IMHO the home page should always be well organized and deliver a strong message about who you are and what you do. Even if people come in on a sub-page, they're likely to visit the home page to get a sense of who they're dealing with.