Evernote is note-taking software in the cloud, with options for private and shared notebooks. Users can take text notes, and upload files to attach them to notes. Evernote has built-in OCR for images with printed or handwritten text. A premium account allows access to notebooks offline, as well as more storage and embedded PDF search.
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Jarnal is an open-source application for note-taking, sketching, journaling, creating a presentation, annotation a document/PDF, and collaborate with others.

MLA, APA, Chicago / Turabian and most-common Bluebook forms as an integrated citing and note-taking platform for individual or group projects. Prompts for analysis of source types and is unique in offering teaching support and personal help on any citation. Instructor / librarian view allows teacher to comment on work-in-progress providing just-in-time feedback in-context. Archives copies of web pages and pdfs which can be annotated. Dashboard provides long-term access to a portfolio of work.

NoteBook is an application that offers a notebook-like interface for organizing digital information. Technical features include the ability to take notes and edit, add sticky notes, copy/paste information, diagram and sketch, annotate, import/export files, and more.

Microsoft OneNote is a digital notebook that allows you to gather notes and information in a central environment, and search across your shared notebooks to better manage information and work with others.

Project Pad is web-based system for media annotation and collaboration for teaching and learning and scholarly applications. Project Pad provides tools for browsing and working with audio, video, and images from digital repositories. The user may organize and annotate excerpts within their own "online notebook."

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.

Skim is a PDF reader and note-taking software, with different colors of highlighting, annotation, sticky notes, numerous export formats and searching and filtering notes.

Springpad allows you to create, organize and share annotations and notes. You may bookmark web pages, search online products, use tags to better organize your information, create your own digital cork-board, and share your information by making your pages "public."