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.

RoSE is a web-based system blending social computing with humanities bibliographical resources, enabling these resources to be explored as a social network. It incorporates data mined from YAGO and Project Gutenberg, offers profile pages for both persons and documents, keywords, and visualizations of the relationships between people and documents. Users are encouraged to contribute metadata supplementing the standard bibliographical data.

Paper Machines is a topic modelling and visualization tool available as a plugin for Zotero. It analyzes Zotero bibliographic collections based on a selection of text mining processes, and enables users to export a variety of visualizations, such as word clouds, phrase nets or heat maps, from the results.