Notezilla - Colorful & powerful sticky notes app for Windows & Phones.

Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.

Laverna - Laverna is a JavaScript note taking application with Markdown editor and encryption support.

Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.

OneNote - Get the OneNote app for free on your tablet, phone, and computer, so you can capture your ideas and to-do lists in one place wherever you are. Or try OneNote with Office for free.

Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.