To introduce my approach to computing and some of the programs I use. I am far from an expert, but I have experimented a great deal and love to fiddle. So use my thoughts only as food for thought and potential targets for exploration.
To record little tidbits for future reference (mainly for my own use). I use some programs or functions only seldomly and often have to go searching for them again. Listing them here is an attempt to make that process more efficient.
General principles
Open source is the way to go. There is no longer any reason to use Windows or MacOS. You can create the same mindless interface in Linux...or you can learn something. (That said, I know it isn't perfect for everyone. And I know switching requires learning, but it will be more useful to you in the long run.)
Throw away your mouse. It is well worth learning keyboard shortcuts for almost every program you use. Much time and flow is lost switching your hand from the keyboard to the mouse and back. Very inefficient. There are still times when it is helpful, but less is more.
Build your own cloud...as far as possible. I pay a host (the exemplary pair.com) to host this website and upgraded for much larger amounts of storage. Through ssh, scp, rsync, and ftp, you can easily run your own cloud. That means less of your data is in the hands of Google and others to process (anonymously, of course!) and you can customize more.
Customizing your computers and clouds is the hotrodding of the 21st century.
Bibliographic managers
If you are going to write papers, use one. I use JabRef, which plays well with Libreoffice. Endnote is quite common and quite good, especially for MS Word.
VIM
An incredible text editor. The learning curve is definitely steep, but well worth it. The main competitor is Emacs. Emacs users and VIM users like to go head-to-head vying for superiority. I have no idea which is better. Nor do I care. I learned this one and it's amazing. Plus, once you've learned the commands, you can find programs that use the same set of commands, making many programs much easier to use. You can use the mouse, but don't. (The GUI version is names Gvim.)
LaTeX
I do my writing in LaTeX. This is not always pleasant, but I would never switch back. You can read a good argument in favor of the LaTeX approachhere.
Use the tex4ht package's htlatex command to convert LaTeX to html. This is particularly convenient for when you have to share documents with people who use word processors.
Statistics - R
For statistics I use R. The great bulk of academic statisticians use R. It is open source. And it will help you more deeply understand what you're doing. (But maybe you don't want to know....) Apparently it has limitations with very large datasets, but (a) I don't use many large datasets; and (b) I'm sure the intelligent user can figure out a way.