When you link to your homepage from internal pages, do you link: site.com/index.php or site.com? Which is more SEO/PR friendly?
You can squeeze a bit more pagerank out of a site by ruling out the index page all together and only linking back to site.com it also stops search engines from getting confused!
I tend to think that linking as site.com is better, that way you get credit for both the internal link and any external links coming in. The external links will almost always be site.com and not site.com/index.htm
correct about the PR, but the other 2 can be solved with a proper canonical 301 if one were inclined to use site.com/index.htm you are correct about the external links. If you decide to make site.com/index.htm the official page via canonical 301 redirects, external links to site.com and site.com/index.html are treated just the same.
You can choose the one you want as long as you're consistent and setup a 301 redirect to the choosen one. But the domain name look better I think