Here you will find an ever-evolving list of links to tools and guidelines that I regularly use or recommend.

Research and publication ethics

Academic Urban Legends Advice for Advisors Ethics of Scientific Publication
Defining the Role of Authors and Contributors Responsible Authorship and Peer Review: Case Studies

Research tools

Zotero (Literature Management) Advanced attachments management plugin for Zotero Better Bib(La)TeX plugin for Zotero SCImago Journal & Country Rank (where to publish)
DOAI (Digital Open Access Identifier) takes you to a free version of the article Creative Commons copyright licenses Open Data Commons GNU General Public License

Thesis resources

A Thesis Proposal Template A Thesis Template How to Be a Good Graduate Student (and advisor)
Ten Simple Rules for Graduate Students Ten Simple Rules for Choosing between Industry and Academia

Scientific writing

The Chicago Manual of Style Online (Writing Style) Publication Manual of the American Psychological Association (Writing Style) IEEE Editorial Style Manual for Authors The ACS Style Guide: Effective Communication of Scientific Information How to Write for Technical Periodicals & Conferences Writing Style and Word Usage Grammar, Punctuation, and Spelling Artwork and Multimedia Instructions
Ten Simple Rules for Better Figures Ten Simple Rules for Writing a Literature Review Ten Simple Rules for Writing Research Papers Ten Simple (Empirical) Rules for Writing Science Ten Simple Rules for a Good Poster Presentation Ten Simple Rules for Making Good Oral Presentations Ten simple rules for short and swift presentations

Latex

The Comprehensive TeX Archive Network MiKTeX (TeX/LaTeX for Windows) LaTeX (Wikibooks) TeX – LaTeX Stack Exchange (Forum)
Texmaker (cross-platform LaTeX editor) Detexify: LaTeX symbols The LaTeX Font Catalogue

Software development tools

Python SciPy NumPy NumPy for Matlab Users matplotlib Spyder (IDE)
Code::Blocks (IDE) C++ reference C++ Programming (Wikibooks) C++ FAQ Lite GDB The GNU Project Debugger Umbrello – The UML Modeller