The simplest way to minimize a window just for a moment?

Solution 1:

Hide the app instead of minimizing.

While in Skim, press ⌘+h on the keyboard. This hides all non-minimized windows of the active application. When you go back (⌘+Tab or clicking in the dock) it returns to where you were last.
FWIW - You can get here the long way by clicking the Skim menu from the menu bar, next to the  menu, and choose "Hide Skim".

Additionally, if you just want to jump to the desktop very quickly you can leverage gestures by "Spread with thumb and three fingers" on the trackpad. Check you system preferences to enable this (See this Apple Support Document for more info Use Multi-Touch gestures on your Mac).

Both of the above solutions become habitual muscle memory very quickly.