I want my application to be unsearchable from the App Store. I would like that only those users who sign in to my web site and then click the link of my iPhone application on ap
To hide your application you have to remove all the App Store countries in iTunes Connect:
To get it back on the App Store, choose the countries where you want it publish.
PS: it might take more than some hours for changes to be reflected on the App Stores.
Since iTunes Connect has been redesigned a bit, go to My Apps > Select your app > Pricing and Availability > Availability (2nd section) > Select Remove from sale.