For example, if I need to run one exe, not in my PATH over some file, I have them both in left and right window. I go to the left, type "Ctrl+F" - e.g. get me the full name (in this case executable), then go to the other window, type "Ctrl+F" again - get me the file to become first argument on the executable and run.
Ctrl+O (in midnight commander too), switches to almost fullscreen command-line - so in a way it's always better than just a command-line.
Search in Files, compare dirs, and many other features (there are tons of plugins).
Also checking SMB shares, FTP, System Processes (though I prefer SysInternals ProcExp.exe there)
I use the Windows Explorer (the file manager) only for very few things - certain context menu items, some forms of preview. It's always there by typing "explorer ." from the current folder.