Scribe, now in version 3.5, is a free note-taking program available for both PC and Mac. Aimed particularly at historians, this program allows researchers to create digital note cards for managing sources, research notes, contacts, images, glossaries, outlines, timelines and more. Furthermore, it enables organization, keyword indexing, searching, linking and cross-referencing of all entries. Entries can be entered directly or imported from online catalogues such as Amazon.com. Information entered in Scribe can be exported directly to Zotero in addition to assembling, printing or copying formatted bibliographies directly from the program. Articles can be stored directly within the program, enabling researchers to search out and highlight particular words within the text in addition to the relevant researcher notes.

Overleaf, previously known as WriteLaTeX, is a free service that lets users create, edit and share their scientific ideas easily online using LaTeX, a comprehensive and powerful tool for scientific writing. Users can start projects with quality LaTeX templates for journals, CVs, resumes, papers, presentations, assignments, letters, project reports, and more.

The DocScanner app uses a device's built-in camera to scan documents. Features include image optimization, OCR, document type recognition (document, business card, receipt, etc.), autosorting, and ability to upload documents to Evernote, Dropbox, and Google Drive.

Referencer is a Gnome application to organize documents or references. You can also generate a BibTeX bibliography file. Referencer is able to automatically acquire bibliographic information (metadata) for some kinds of documents once the file (usually PDF) is added to the library.

Qiqqa is a research management software that allows you to organize large numbers of papers; find new papers to read and new information about papers you already have; review materials and create annotation reports. Qiqqa has several PDF tools that also allow you to convert from PDFs to text, and use a clipboard function to cut and paste text into your document.

DEVONthink is a database that helps users organize, manage and collaborate on digital files, including Office files, links, e-mails, research data and PDFs.