Hi there and thank you for your question.
Basically everything that has a link (does not need to be an HTTP link) can be part of the App Center. This is a very powerful feature as it allows you to deep link into any software and to any element there, if the software and the client support it. The condition is important here. The client needs to support it.
So if you want to open a specific skype conversation, there are two requisites: 1. The app / software needs to be installed on the device. 2. The software itself needs to allow you to deep link. Otherwise you'll only see the start screen of the software as when you open it.
The best practice today is to always link to a HTTP link and try to offer a "open in app" link if the app / software is installed on the device then. Some apps like "facebook" or "quora" will automatically open the app from the browser then, if installed. Intercom for example lets you explicitely decide what to do.
If you are sure, that a software is installed (like on a thin client or a remotely controlled software managed device) you can directly open the app / software). The App Center does allow you to enter personalized entries. So you can have a HTTP link for all and a direct link for all who have thin clients for example.
It is impossible to say, what the standard best practice is. It really depends on your setting in your company. Do you have thin clients? Do you control what software is installed on your employees computers? To what extent? Do you have corporate smartphones that you control? Do you support a bring your own device concept for smartphones? All of this plays a role to find the right answer. We're here to help you. We also have partners right next to you and would want to give you a contact to one of those as well, so that you have someone right on site if needed and wanted.