Our navigation was written in plain html, and includes over 100 links to our internal pages.
The navigation appears on the bottom of every page, with the exact same links on each and every page.
So we got all information about the page at first, and beneath the page contents we currently have our entire navigation (drop down menu) listed in plain text followed by links. The navigation includes most of our keywords and anchor text to that specific page as well.
I have seen cases like these, where too many same links/content, can lead to duplicate content problems. It also depends on where in the source code of your html code these links are, and what is the ratio of the "unique" content on the page, vs the navigation links?
If you are using drop down menus created using js then it may be justified to have all those plain html links at the bottom. However, as Nakulgoyal mentioned, make sure the unique content vs. links ratio is well tuned or some of your pages may be considered as duplicate content (the ones with the less ammount of content). Not terribly dangerous but better safe than sorry ;)
I doubt that 100 links on a page would be the cause of going supplimental. Just look at all the amazon(dot)com links on a page or some of the others.
There is another underlying cause for going supplimental. You may have duplicate content ... or at the very least similar content, or you could have the same title and description on the page. Without knowing your url i'm just throwing out some guesses.
Have you made sure someone hasnt copied your content? Are you using manufacturer descriptions?