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DEVONthink - DEVONtechnologies develops DEVONthink, DEVONagent, and other Mac and iOS apps for document and information management and web research.
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.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
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.
HoudahSpot - Advanced File Search Utility for Mac OS X
Google Keep - Capture notes, share them with others, and access them from your computer, phone or tablet. Free with a Google account.