draw.io - Online diagramming application
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
LucidChart - LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
PlantUML - PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams.
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.