Day One - A simple journal application for the Mac, iPhone, and iPad. AboutTo learn more about Day One, see these two excellent reviews . PublishPublish is not available in Day One 2.
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.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Reminisce Journal - Reminisce Journal is a free iOS and Android app that helps you to capture live moments, daily activities, thoughts, ideas and travel logs, etc.
Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.