I do more than just dev work. I also do sys admin work. So a lot of the tools that I use are for that as well.
For a VM I like virtualbox - it’s simple enough and does what I need from it
I use VIM on the cli and SublimeText for working on anything that involves text - be it coding or configuring a system.
For version control, git is awesome. I like to use the gui from github on the mac - as it just makes it easier to deal with. I have setup a gitlab repo at work for and on that I use the cmli with the .ssh/config setup to make it easier.
I did like Evernote - but started to worry about what I put in there. So I stopped using it and moved to Zimwiki for my documentation. I don’t really have a notes workflow at the moment. Right now, I’m using a cron job to sync my zimwiki files back to a gitlab installation for backup and version control.
For databases, I usually cli it - but have used workbench from mysql. On my mac, i use Sequel Pro - it’s fantastic.