Pliny was a tool for working with annotations when conducting personal scholarly research, and can be used with both digital and print materials. It also had data manangement and organizational features, and was designed to facilitate reading, reacting to that reading and forming an interpretation. Pliny stored all data on the user's computer rather than remotely on the web.
Paperpile is a web-based commercial reference management software with special emphasis on integration with Google Docs and Google Scholar. It imports data from academic publisher websites and from databases such as PubMed, Google Scholar, Google Books, and arXiv. Paperpile can retrieve and store publication PDF files to the user's Google Drive account.
Citavi's core features are reference management, knowledge organization, and task planning.
Reference management
Search in thousands of databases and library catalogs from within Citavi
Organize references
Annotate and automatically rename PDF files
Batch import PDF files and import their metadata automatically
Find fulltext to references
Collaborate with others on a local network (no need to have your data in the cloud)
Import from other reference management programs and formats, including RIS and BibTeX
Import ISBNs, DOIs and PubMed-IDs on web pages with a click
Import web pages with a click
Transform web pages into PDF files to save their content
Work seamlessly with Word (versions from 2003)
Send references to Open Office and LibreOffice Writer and any program that can process files in RTF (i.e. Scrivener)
Use with LaTeX editors
Create subject bibliographies with a click
Publish in all common citation styles. Styles for journals can be requested" target="_blank" for free
Integrated citation style editor
Advanced style finder
Integrated quick help
Interface and quick help in seven languages (English, French, German, Italian, Polish, Portuguese, Spanish)
Knowledge organization
Import text excerpts and images from documents as quotations and organize them together with summaries, comments and own ideas imported as "thoughts"
Quotations, summaries, comments and thoughts can be outlined directly in Citavi to reflect the structure in chapters of the publication prior to the actual writing, thus permitting to separate the construction of the argumentative structure from the actual writing process
Task planner
Schedule tasks related to titles (order, photocopy, extract citations, read, check, ...) and milestones
Print lists of to do lists with a click
Zotero is a free tool that collects, manages and cites research sources. It stays on your web browser where you do your work and it's easy to use. It's being downloaded as a firefox extension, used with the chrome and safari browsers or used as a standalone tool. It allows you to attach pdfs, notes and images to your citations, organise them into easily searchable collections for different projects, and open office using any of over 2800 citation styles. references can be added to a zotero library in many different ways: directly from databases, journal websites, google scholar or the library catalogue, by referencing file import ( for example from an Endnote library), by dragging in pdfs from your hard drive, and by entering them manually.
LitBlitz is free beta Chrome extension that aims to improve how students and researchers manage their notes for literature reviews, assignment research and more by simplifying pdf management, allowing capture and annotation of document snippets
LitBlitz v1.0 is currently available as a Google Chrome extension.
LitBlitz, while still available on the Google Chrome store (https://chrome.google.com/webstore/detail/litblitz-speed-up-your-li/ohmfdhillclkchlgoifgokmdjhonmgao?authuser=4&hl=en) no longer appears to be under development, and the company url redirects to a Japanese language web page.
Tinderbox is a personal content assistant that helps you visualize, analyze, and share your notes. Tinderbox provides maps, timelines, charts, and outlines to help you view and organize your information.
The Annotator allows you to analyze any block of text created by other authors. You may use virtual markers to highlight important passages, questions, thoughts, or add comments.
SharedCopy was a tool developed by Choon Keat, allowing users to individually and collaboratively annotate webpages. SharedCopy worked with platforms including Twitter and Basecamp, and enabled integration with other online services via its API.
Scribe is a note-taking program that allows you to manage your research notes, quotes, thoughts, contacts, published and archival sources, digital images, outlines, timelines, and glossary entries. You can create, organize, index, search, link and cross-reference your note and source cards.