I'll echo what others have said; my top ten changes, but my top two never do. These are the episodes I gravitate toward these days. Not in any order except for the first two.
The Doomsday Machine
Where No Man Has Gone Before
The Enemy Within
The Man Trap
A Taste of Armageddon
Mirror Mirror
Day of the Dove
The Tholian Web
Journey to Babel
Bread and Circuses
The Doomsday Machine
Where No Man Has Gone Before
The Enemy Within
The Man Trap
A Taste of Armageddon
Mirror Mirror
Day of the Dove
The Tholian Web
Journey to Babel
Bread and Circuses