[microtonal]

I fully agree. There is a place for both. Even though I use TikZ every once in a while, if I need to draw some graphs really quickly, nothing beats a GUI program like OmniGraffle. Or if you need to touch up a photo, you could spend a lot of time tinkering with Imagemagick, but it's much easier to just fire up Lightroom or Pixelmator.

Even for editing, I sometimes prefer GUIs. E.g. X11/Cocoa emacs can render LaTeX equations inline in AUCTeX or org-mode. This is sometimes very convenient for quickly verifying whether equations are correct during writing. Similarly, with org-mode, you can show R or gnuplot graphs inline.

On the other hand, when you are automating a build, doing some custom data extraction, configuring a server, etc. nothing beats the command-line.

A skilled person knows what to use when.