Mike,
How many keywords are you optimizing for? If we're talking 100's/1000's, I would personally tend to lean towards pointing towards the most relevant content on your site. This will up "time on site" and lower "bounce rate" because the content the user just clicked the anchor text of will be more relevant than pushing them to your home page and having to search allover again. How many times have you clicked a random link only to be pushed to a home page and thought, "Well hell, I'm not going to bother!"
You should have a base set of "core" keywords you can target for your root domain.
Hope that helps,
dan
