JS_Harris - 9:51 pm on Feb 6, 2010 (gmt 0)
I'm assuming you mean you have a link to your homepage sitewide and are ADDING an extra link on the homepage with choice anchor text? If so...
Run a test, kill the link and see what happens.
I think you're ranking well because search believes you when you say the page is about red widgets, not because of the link but because A) the page text is about red widgets and B) your index page has the highest value on that domain which beats out other sites inner pages.