Zotero is a free and open-source reference management software to manage bibliographic data and related research materials. Better BibTeX (BBT) is an extension for Zotero and Juris-M that makes it easier to manage bibliographic data.
I have been looking for a simple and flexible tool to manage projects, take notes from reading (e.g. literature and online), and track results of data analysis, e.g. EverNote, OneNote, Trac, JIRA, github, RMarkdown, etc.