Group List together under site content

In the Site Contents, there is not a way to group them together. However, once they are created you can create a "Department Documents" list that links to each of the lists and libraries you're creating. In THAT list you can add additional columns for meta data to filter the list. For instance you can have a column to identify if it is a list, library, playlist, etc., then create a view for each of those types of lists. Another column could break it down by type like training, policy, procedure, forms, templates, etc., depending on how you're creating the sites, libraries. 

The bonus to using the master list is that you can then create a SharePoint page, or use the main site page, to embed or link to that list. That way department users can quickly and easily filter to find the library they're looking for and link directly to it without having to link EVERY list and library in the navigation or on the page.