Default pop-up menu in JSmol 14.6.2:

Problems:

• menu is too tall overall
  • spacing may be reduced using

    ul.jmolPopupMenu , ul.jmolPopupMenu ul { line-height:1em; }

  • checkboxes make lines taller; use this:

    .jmolPopupMenu input[type="checkbox"] { transform: scale(0.8); margin-top:-0.2em; }

• language menu is too tall, the bottom part may be unaccessible
  • make a limited height, scrolling submenu

    .jmolPopupMenu ul.ui-menu { max-height:25em; overflow-y:auto; overflow-x:hidden; position:fixed; }

• bad encoding in language names (only in the original language string)

Sample 1   (on a 500px JSmol panel):