Evernote

Note-taking app that runs on all major operating systems.

Mendeley

Mendeley assists at every stage of the research process, from gathering research and annotating PDFs to organizing citations and creating bibliographies.

Noodle Tools

An open source language and environment for statistical computing and graphics. It has both the flexibility and steep learning curve of a programming language.

OneNote


Web-based, collaborative software for gathering notes, drawings, screen clips, and audio.

PowerNotes

PowerNotes is a web app that helps with online research -- gathering and keeping track of source materials, staying organized, and creating a research outline.