How to remove other apps icons (like Skype or WhatsApp) from contact and phone app? I would like to keep Skype Mobile installed but get rid of its icons from contacts AND/OR from being asked whether I want to make a call to the contact through Skype or other similarly annoying application. Is there any facility in Android that allows me to keep the control of that? Uncle Google isn't much helpful in that matter.

Moreover I have two Skype icons per contact on my phone. And that the thing that hits my taste.

Phone details: Sony Xperia S, Android 4.1.2
go to Settings > Accouts and choose Skype/WhatsApp > then search for each one how do you remove the sync contacts. After this your Contacts list should update not showing Skype/WhatsApp data.

As for the call using skype, you should have the option to choose Phone and click Use Always.

This is very phone dependent, so if you cannot find this options, tell us more about your phone and Android version.