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Laverna - Laverna is a JavaScript note taking application with Markdown editor and encryption support.
Todoist - Todoist is a to-do list that helps you get organized, at work and in life.
Notezilla - Colorful & powerful sticky notes app for Windows & Phones.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
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.
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.