I think you must basically stick to simple rules when it comes with a homepage, which represents the location where everyone gets the direction he wants.
I think you may want to make the distinction between informative boxes (latest forum threads, search engine at the top, ...) and boxes containing pieces of information exclusively concerning the website (such as the menu, the latest news, the login/pwd box). Ergonomically speaking, I think it has a strong role in orienting people. You should look at what most websites do and just mix to make your own. You don't have to reinvent the wheel, what works now and what is popular now is just a big advantage for you : the guys have already reflexes to instinctively search for the right function at the right location. Your advantage is that you can observe what is done around and simply do the same. Plus, take in consideration that in ergonomy, generally speaking, one should reach his final destination within your website in a maximum of 3 clicks.
Remember, keeping the actual way of creating websites is important, that's why the W3C also try to make norms, that's to implement automatism in people's mind so that one may find the function he needs in a view in any website, that's not only the common programmation recommendations (HTML, HTTP, XSL, ...).