Evernote - Bring your life's work together in one digital workspace. Evernote is the place to collect inspirational ideas, write meaningful words, and move your important projects forward.
Todoist - Todoist is a to-do list that helps you get organized, at work and in life.
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.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Google Keep - Capture notes, share them with others, and access them from your computer, phone or tablet. Free with a Google account.
BibDesk - BibDesk is an organizational software created to help you edit and manage your bibliography. It keeps track of your bibliographic information as well as said information's associated web links and files. Read more about BibDesk.