Emacs. I came to Unix from an MS-DOS background, where I used Norton Commander (of which Midnight Commander is a key-for-key clone), but I ended up not using MC. It turns out you just don’t use Unix the same way as MS-DOS. When I need to manipulate files in any quantity, I use Emacs and its dired-mode.

See especially the “wdired-change-to-wdired-mode” command – it’s magical.