In addition to many excellent suggestions (thanks) in the article and the preceding comments, perhaps I could just mention Emacs; the UnxUtils collection of native (not cygwin) core utils; the whole of the rest of the suite that ProcessExplorer belongs to (Autoruns, Handles, Sysmon, PSservice etc). Also something for mounting ISOs is nice (I use VirtualCloneDrive), and on the subject of disks, I love WinDirStat and its graphical representation of how storage is used (roughly equivalent to Linux's Baobab). And is it just me that loves Q-Dir as a Windows Explorer replacement?
I also like to have a few extra command-line binaries like sha256sum, base64 etc.
(Probably just me, but I always have GnuPlot, GeoGebra and a free Smalltalk development environment - such as Squeak or Pharo - as well)
And - not an application, but any windows system I use, first thing I do (ok, after installing a Dvorak keyboard YMMV) is to put the task bar up the left hand side, with small icons, so you can actually read what the windows are! And what else are you going to do with all that horizontal space when the vertical resolution doesn't allow 2 A4 sheets side by side?