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My question is does it matter if you link to yourself by [mysite.com...] or [mysite.com...]
Does the index.htm make any difference at all?
When I check my pages, mysite.com/content/index.htm has the same PR as mysite.com/content/ , and as long as I can remember (which is not long actually), it's been this way. So I think "no" is the answer to the original question.
Maybe there is some confusion with the "www" prefix issue. I believe that www.site.com and mysite.com are treated separately by Google.
Be safe and just link to the domain.
If I provide a path like this...
www.example.com/ or www.example.com/sub/
That is what the spider based SE's seem to pick up minus the index.htm. So, if I ever switch over to a .asp home page for the directory, I'm hoping that my link path structure will allow me to make that change and not have to worry about setting up a 301 from the .htm to the .asp version. Are my assumptions correct?