gouri - 4:12 pm on Mar 7, 2013 (gmt 0)
Navigation links are definitely listed. But then, I don't know how good search engines are at identifying navigation sections. If it's a widely used CMS that comes with something like "id = 'navheader'" then maybe, but otherwise how can they tell?
Maybe the links that are shown are based on the quantity, and not so much on where on the page they are located.
Would you say that same-page anchor links are counted as an internal link, just based on your general opinion of how links are looked at?