Google and Yahoo both make a difference between Inbound Links to yourdomain.com and yourdomain.com/Index.HTML pages. If you want to see the diferences please make a manual URL named yourdomain.com without the index.html extension and compare the two. This also makes clear that Link to your root and to your index have a different Link Popularity or Pagerank as Google names it. So when asking for a link back, decide if you want this to be your root or your index page and stick to this!