A nice thread at High Rankings forum discusses Internal Linking To Your Homepage. A basic SEO topic, but also very important. What is the best way to link to your homepage? In my opinion, http://www.domain.com/ is the absolute best way. You can link to it using absolute links or relative links, but link to it so that you do not link to http://www.domain.com/index.html, http://domain.com/index.html, http://domain.com/ and so on. You just want the www, the domain and the / and nothing more.
You may ask, but what if I always link to http://www.domain.com/index.html type of domain? As long as I am being consistent, isn't that good enough. Well, yeah it is, but can you guarantee that you won't upgrade your site's technology and the index.html page will turn into an index.php page? Of course you can do mod_rewrites and 301s after the fact but if you are just consistent, with linking to http://www.domain.com/ you don't have to do all that work. Plus most people will link to you with http://www.domain.com/ and no other way.
Forum discussion at High Rankings Forums.