Boring, realistic explanation: Male characters in Star Trek: The Original Series are wearing visible eyeshadow in some shots because 1966 was right in the middle of the transition from black-and-white to colour television in America, and TV makeup artists were still adjusting to the fact that stage makeup is easier to see in colour broadcasts.

The truth we know in our hearts: Male characters in Star Trek: The Original Series sometimes wear eyeshadow because the future is fabulous.