When you deploy Windows 8.1 on computers which have a Wifi adapter, there is a step in the Setup Wizard to choose the Wifi network, even if ethernet card is active.
This step can block a SCCM task sequence or a MDT deployment because the Wizard asks for an action.
Fortunately, this step can be bypass/disabled by using an unattend.xml file.
With System Center Configuration Manager 2012, there is a new functionality: Application Catalog. Using Application Catalog, you can deploy an application on user collection, and all users can use this web page to install or request an application.
To launch the Application Catalog, you can use the existing link on Software Center:
Link Software center
Depends on your system configuration, Internet Explorer can prompt for your login / password. Even if you are in your domain.