I'm trying to keep notes on all the tools that are part of my development and workflow, as well as the bits that tie everything together online. This is difficult, especially some of the small bits online, so this is an ongoing list to remind me. And readers can consider this a conditional endorsement, I'm happy to chat about my experience with any of them.
Everything lives in Github -- everything. Code, papers in progress, presentations, even this lab notebook. Usually data, but if it's too big for Github, it's on S3 with links here on Github. I've been using Unix variants for almost 30 years, so generally my tools rely on "composable" things like shell commands, Makefiles, and plain text, but there are undeniable advantages to working with a modern IDE for a complex piece of code. JetBrains makes the best IDE's around for general purpose programming languages, RStudio is great and improving daily and Wolfram Mathematica is essentially when you need symbolic mathematics.
Nowadays, I write in plain text a lot, using Markdown and RMarkdown as a "source" language for documents, and then I turn them into PDF versions (often via a LaTeX intermediate). But I still write a lot of LaTeX directly, which I have a soft spot for. And I think Microsoft Word is ugly and clunky, and it makes certain things like uniform document structure, automatic cross references, bibliography management more complex than they should be. It's gotten better in recent years, and Endnote or Zotero or Mendeley are essential if you write in Word a lot. But I don't, and BibTeX is a universal format in the sciences, and BibDesk is a great and open source tool.