TheOptimizationIdiot - 5:10 am on Mar 9, 2013 (gmt 0)
If it is an over optimization penalty though, why the homepage?
Because the algo looks much more at "site as a whole" rather than independent pages now, and if the internal pages are penalized for some reason it can have an effect on other pages, including the home page.
and why on earth would I receive such a harsh punishment of being deemed spam in the back of the serps?
It's an algorithm, not a person looking at your site. It's relatively "black and white" and if it "finds a spam pattern" (which is basically what it has to determine over-optimization is) then it treats it as spam, even if the site is not what we as people looking at it might think of as spam if we were to visit it.
One thing to keep in mind is it's really not personal.
The determination is made by a scoring system when determining a score for your site and it determined something was "wrong" or "didn't score well" with it from an algorithmic perspective, not a "personal" perspective.
It has no clue how many hours you've put into it or how many questions you answer or how great your customer service is or anything else along those lines. All it sees is source code and inbound links and other "signals" relating to your site that are generally publicly available.