In essence they all do the same three things:
1. Store information about books, articles, websites, etc. in one place.
2. Organize this information in a useful way and make it searchable.
3. Use the information in your reference manager to add in-text citations and a reference list to a document you are writing or to create a bibliography.
They vary in many details.
We will focus on 4 (EndNote, RefWorks, Zotero, F1000). There are many others available (relevant alternatives include Mendeley, PaperPile, Papers merged with ReadCube). As I write this in August 2019, Papers is now a subcription service costing $36/yr for students and $60/yr for academics, Elsevier/Mendeley began to encrypt the data in your library without your consent. Initially it was almost impossible to move your Mendeley library to another product but to their credit this problem appears to be resolved. Zotero, F1000, PaperPile and RefWorks work with GoogleDocs. RefWorks and F1000 are free to you as a UCSF person, Zotero is free to all unless you need to buy extra cloud storage space, Mendeley costs money is you try to form a group of more than 3 people. You pay a monthly fee for PaperPile. We try to monitor developments in reference managers and will provide information about significant updates.
These points refer to EndNote, F1000 Workspace, RefWorks, Zotero and Mendeley:
This is an attempt to provide a brief overview of five popular citation management software. The right software for you will depend on your work and your environment.