Zotero

Open your Zotero application. At the top left is a folder button with a green plus sign. Click this to create a new "collection."

Create collections to organize your references. Collections are like file folders on your computer, but a reference can be in more than one collection at a time.

In other words, a book on Civil Rights in the United States could be filed in your "John Lewis" collection, your "Freedom Riders" collection, and your "1960's America" collection without having to make three copies of the reference.

Adding tags to your citations is another way to organize them. By assigning tags and colors to articles, you are giving them "keywords" to characterize the articles in whatever means you desire. 

You can tag items based on their topics, methods, status, ratings, or even based on your own workflow (e.g., “to-read”). Items can have as many tags as you like, and you can filter your library (or a specific collection) to show items having a specific set of one or more tags.