"One of Our Planets is Missing": Some nice drama with the danger to the colony and Governor Wesley's sense of helplessness, and a good, classic Trek story of facing a "monster" and building understanding and peace with it rather than destroying it (also a perennial theme in Filmation's overall body of work). Although it's right up there with "The Changeling" in its parallels to ST:TMP (giant cloud endangering human planet, the ship traveling through it to its brain, Spock melding with its brain).
"Once Upon a Planet": A neat "Shore Leave" sequel that fleshes out the workings of the amusement-park planet and gives Uhura a chance to shine.
"The Time Trap": The "cooperate with the Klingons" story is a neat idea, and the diversity of the Elysians is interesting. Kor's return is welcome, though I regret that they couldn't get John Colicos. It's good to get another female Klingon in Kali, and Devna is noteworthy as the only 23rd-century female Orion character to be portrayed as sane and intelligent (although she wore even less than her predecessors Vina and Marta).
"The Slaver Weapon": A surprisingly faithful dramatization of Larry Niven's "The Soft Weapon," so much so that I don't even consider it a Star Trek episode, but a Known Space pilot acted out by three Trek characters.
"The Jihad": The premise is kind of fanciful and the title is problematic (the threatened holy war is more a crusade than a jihad, properly), but the idea of a diverse team recruited for a secret mission is interesting, as are the new characters on the team (including what's basically Kirk's only romantic interest in TAS, if only barely). The Vedala are also intriguing, and I would've liked to see more of them (which is why I wrote them into DTI: Forgotten History).
"Albatross": A great McCoy story and an effective drama. Only two complaints: One, the idea of auroras in space is silly (they're atmospheric phenomena), and two, it doesn't live up to TAS's mandate of doing stories that couldn't have been done in live action. With a more humanoid design for the Dramians, this could easily have been a TOS episode.
Honorable mentions:
"Beyond the Farthest Star": The alien ship is a fantastic design.
"The Survivor": Cool to see a female security officer, even if she's defined mainly as a love interest. And the Winston-Vendorian is a good character.
"The Magicks of Megas-tu": I'm torn. It's a good anti-prejudice statement, even subversive in its positive portrayal of a "Satanic" figure, but it somewhat misappropriates the Salem witch trials (though not as badly as most fantasies involving them) and it's rooted in an outdated and debunked theory of cosmology.
"The Eye of the Beholder": Alien-zoo stories are a dime a dozen, but the Lactrans are cool.
"The Pirates of Orion": Pretty effective drama, and our one pre-ENT look at Orion males, but their weird coloring and the weird mispronunciation of "Orion" are off-putting. I actually prefer Howie's second story about choriocytosis, the early Pocket novel The Covenant of the Crown.