Robert_Charlton - 11:33 pm on Jun 28, 2012 (gmt 0)
I suspect this could be a penalty for 'spammy' backlinks. We have too many backlinks using the same anchor keyphrases.
Did you notice when the traffic drop happened? The Penguin update launched on April 24.
What percentage of your backlinks, would you say, were using the same-keyphrase anchor text? And how did you get the rest of your backlinks... ie, what kind of links are they?
Is there a way to combat this kind of penalty by diluting the anchor keywords (getting bigger variety of incoming anchor keywords)?
The problem with trying to build links to get out of such a situation is that if you don't have content that might normally attract good links, you'll have to resort to artificial ways of getting new links... and it's likely that Google will detect those, particularly now that you're already on their list.
Things to check regarding your situation in the index...
You might try searching for a unique string of text from your site's home page... say roughly six to ten words... and put it in quotes.
Have you tried a site:yourdomain.com search? Does your index page appear?
Also, check your home page for various possible canonicalization issues.