I use the following software, happily.
- Chrome, great sync across machines and hand-helds, fast, simple, add Vimium if you like Vim and Disconnect for faster and more secure search.
- Jekyll to generate websites.
- Vim, all-purpose text editor.
- Pandas, powerful python package to analyze large datasets.
- Python, scripting language to prepare raw data and conduct statistical analysis.
- Reveal.js, flexible framework for HTML presentations.
- Useful Mac software:
- Ipe to create (vector) graphs (easily imported in latex).
- MacTeX to use latex.
- Skim to read and annotate PDF.
- TextExpander to save on keystrokes.
- Awareness to not forget to take breaks.
- Skitch (classic) to make screenshots, annotate them, and share or save them (this is the last version before Skitch was bought by Evernote, later versions were effectively downgrades).