To better understand Gene Roddenberry’s vision for Star Trek, here are the ten episodes he told TV Guide were his favorites.  He listed these episodes just two months before his death.

Amok Time

Balance of Terror

The City on the Edge of Forever

The Devil in the Dark

The Enemy Within

The Menagerie, Part I and Part II"

The Naked Time

The Return of the Archons

Where No Man Has Gone Before

The Trouble with Tribbles