Well, just from TOS, the episodes that take place inside the federation are ... Mudd's Women, The Man Trap, Charlie X, Balance of Terror, Dagger of the Mind, The Conscience of the King, The Galileo Seven, Court Martial, The Menagerie, Arena, The Return of the Archons, Space Seed, The Devil in the Dark, Errand of Mercy, Operation - Annihilate, Friday's Child, Amok Time , The Doomsday Machine, The Apple, The Deadly Years, The Trouble with Tribbles, Journey to Babel, Obsession, A Piece of the Action , The Ultimate Computer, For The World Is Hollow, And I Have Touched The Sky, Let That Be Your Last Battlefield, Whom Gods Destroy, The Lights of Zetar, The Cloud Minders, The Way to Eden.
You might be able to contend whether a few of those episode aren't "the best," but they are inside the federation. (please excuse me, if a few were outside in your mind)
I was actually a bit surprise when assembling the list how many TOS missions were inside.
