10. The Menagerie - Parts I & II (1.11/1.12)
In addition to being the one and only two-part episode of the entire Original Series, which already makes it stand out, The Menagerie was also a very crucial episode in the production of Star Trek itself, as it provided the show's crew with some much-needed breathing room.
Due to how intricate the show could often be, Star Trek was struggling to meet its deadlines, with episodes being completed and sent off to NBC only days before they were set to air, with closer and closer calls each week.
This naturally put a great amount of stress on both sides, until Gene Roddenberry had an ingenious idea. They would make a two part, flashback-oriented episode that would be made up mostly of unused footage from The Cage, the aforementioned unaired pilot.
Not only would this make the two-part episode quick and easy to shoot, but would also give them a much bigger window of time to produce the new episodes that would come out from there, which was not only good for Star Trek's crew, but also likely help put the people at NBC at ease.
The Menagerie has gone on to be considered one of the better episodes of TOS in its own right and has even been given special theatrical screenings over the years.