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On page factors are also OK , it can be due to over optimization of keyword through link building (this can be true for first case but still I need some concrete stance and what can be done to remove the same)

but second case is not at all understood.

I don't think this is domain crowding , DC occurs when front page lists more than 2 separate listing in the serps , but this is proper structure of a website shown with help of xml (if am not wrong) , so Google must be pulling that data from somewhere and structuring the same dynamically ( or grabbing it from sitemap) am not sure abt that .... that's why I posted this question.  At first I thought that this is happening for very high traffic and reputable websites(Google is listing top pages of the website as tabs) , but this is not the case ,

one of my clients website ( which is quite new with 25 domain authority and no alexa rank) also shows in the same manner on its anchor keyword, maybe someone who has actually dealt with it can give a better answer.

I have been searching around but unable to gather information as to how we can control or list  top pages of a website on Google's first page , i.e. if we type seomoz in google , we can see the main listing with 6 subdomain listings , which link to Blog , Seo tool , Beginner Seo guide , Learn Seo , Pricing & Plans and login

My question is can we control these listings i.e. what to display and what not , and if yes how can we make this type of visibility on first page , by using html or xml sitemaps or theirs something mostly websites are missing. Cause this type of data is coming up for very less websites and mostly websites are with single urls.

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well according to me if you have taken the website down and pages are removed , then you don't need to redirect them to 404 , i.e. if something doesn't exists its automatically redirected to 404 , first thing you can do is remove those links from webmaster tools via remove tool and robot.txt file , ( it will take some time but the links will be removed ) secondly if you are worried about 404 and want to redirect it something meaningful , in my opinion that would be better idea , just redirect all the pages which don't exist to a single page displaying

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I hope this helps.