I am working on one e-commerce website for last 8 months. Site was running smoothly and traffic was also good enough as per the new site. All my important pages got top ranking withing 3 months. But then after 5 months this website got struck with any Google penalty and lost all the ranking. Traffic reduced by 90%. And to recover this penalty it took two months. Now the site again back on the top. But the problem here is the index page. The page is cached in Google but not getting ranking in Google SERPs not even for any unique key phrase or long sentence. Not getting exactly what happened with the index page? If there would have been any kind of link penalty and all the other pages have out of the penalty then index page also should have come out of penalty. As far as on site optimization is concerned, it is well optimized. It has also got good link popularity. Sitemap is showing no error. I didn't add robots.txt, i don't think it is really needed as such. Any body faced the same situation or any body having any idea what the hell happening with the index page, please kindly share.
You mentioned that your site already got penalty. So Google will penalize your site by reducing SERP ranking and also do delsting from SERP.
So you mean that only sub-pages appear in searches? It's just the index that won't appear? As a test, I might suggesting trying to promote the index and a subpage with Adwords. Use the adwords interface to see what kind of quality score Adwords assigns to the index page compared to the sub-page. To follow up, try pointing another domain at the same content and test that the same way. If Google gives the index a better quality score on the second domain, then there's a pretty good chance that it's a purely domain related penalty. Either way, that kind of testing should give you an idea of which direction you need to work in.