In your ApplicationName_reg.rss file you will find a structure RESOURCE APP_REGISTRATION_INFO. You need to add the following line to the resource.
BYTE hidden = KAppIsHidden;
This application will be a hidden application, and it will not be shown in the Applications list.
RESOURCE APP_REGISTRATION_INFO
{
...
hidden = KAppIsHidden;
...
...
}
Please read the comment section.