Not to nitpick but Roddenberry didn't write most of the episodes you have listed; he only came up with the idea which he called "springboards". The "springboards" were only a sentence or two long which could be given to a writer to come-up with a story. Really he only wrote "The Menagerie" and "The Omega Glory" all others you have listed were written by other people or Roddenberry with someones help.
"Mudd's Women" was written by Stephen Kandel
"Charlie X" was written by D.C. Fontana
"Corbomite Manuever" was written by Jerry Shol
"Return of the Archons" was written by Boris Sobelman
"Bread & Circuses" was written by Roddenberry & Gene Coon
"Assignment: Earth!" was written by Art Wallace
"Turnabout Intruder" was written by Arthur Singer
"Encounter at Farpoint" was written by D.C. Fontana & Roddenberry (and David Gerrold if memory serves)
So, saying all of THAT, I would have to vote for "The Menagerie" since that's about the only one he really wrote himself without other writers (even though John D.F. Black wrote a nice version of it before Roddenberry did)
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