Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.
Citavi - Citavi is a program for Microsoft Windows that manages literary references and organizes organizational knowledge.
OneNote - Get the OneNote app for free on your tablet, phone, and computer, so you can capture your ideas and to-do lists in one place wherever you are. Or try OneNote with Office for free.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
Standard Notes - A safe place for your notes, thoughts, and life's work