Our web site traffic has been dropped 90% for second time within recent six months. The first time some of pages with address niazpardaz.com/search dropped, the second time same pages with address niazpardaz.com/sa dropped and the whole website get penalty and its rank has been dropped too much. Our site is cleaner than our competitors and we review and respect all rules mentioned in Google guidelines but we didn't find any reason for this penalty and so in the future we can not prevent its re-occurrence.
A few thoughts:
A "cleaner" site is not only subjective but it is not a ranking factor. It can indirectly affect a page's ranking as a poorly built website will be harder to use and thus attract less links. But by itself it is not a ranking factor.
If this has been happening to you recently then the odds are you are falling victim to what is known as the "Panda algorithm". This is Google's attempt to weed out low quality content. If you haven't done anything that violates Google's terms of service, and you are sure that your pages are optimized, then this is a likely culprit. The only real way out of it is to make sure you have quality original content in your website.
Have you signed up for a Google Webmasters Tools account? If there is a problem with your website Google may notify you through it.
It's hard to answer as I don't read Persian, but based on your question I can tell you that Google does not like to include search results from other sites in its results. They used to include these pages but stopped when the comparison shopping sites started setting up canned searches as web pages and Google did not like seeing them in their results.