A week ago I decided to add a CSS drop down menu to the header of my site which of course has added tones of links to every page of my site. This morning the site has disappeared from the serp. The first thing that's crossed my mind was to remove the drop down menu. I can not possibly think of any other reason for the penalty. My site has been ranking quite well for the last 2 years (enough for what it is and for me :)). I'm not sure if this is a penalty actually, because my PR is still 4 as it used to be and if I search for the domain only - the site is steadily on the first place. Some of the pages which have not been indexed with the drop down menu are still ranking on the first page for their keywords. But my home page and 90% of the pages have gone from first page to +10 page in the search results!
I'd like to ask if it's possible to get such a penalty and if Google treats the navigation menus as link farms or key words stuffing.
And if this is actually a penalty or some kind of a filter has been applied?