A dictation application that can be trained to recognize your voice and specialized vocabularies.
Note-taking app that runs on all major operating systems.
Mendeley assists at every stage of the research process, from gathering research and annotating PDFs to organizing citations and creating bibliographies.
An open source language and environment for statistical computing and graphics. It has both the flexibility and steep learning curve of a programming language.
Web-based, collaborative software for gathering notes, drawings, screen clips, and audio.
PowerNotes is a web app that helps with online research -- gathering and keeping track of source materials, staying organized, and creating a research outline.