I'll go ahead and post the complete articles. I'll do one a day so there's no overwhelming, although it will mean no surprises for the first couple of days...
In this first article, I will discuss the best and worst episodes for each of the three seasons of Star Trek: The Original Series, the two seasons of the Animated Series, and the classic movies (I-VI). For the three 7 season episodes, I will divide each of those into two entries, and then finally cover the 4 seasons of Enterprise.The movies from Generations to Nemesis will be covered in part 2 of the entries on The Next Generation. For two part episodes, they will be counted as one episode, and if they're season ending cliffhangers, I will count them under the season part 1 happened in.
So, off we go:
STAR TREK: THE ORIGINAL SERIES:
Series overview: The original and best. Originally marketed to networks as "Wagon Train to the stars", Star Trek was really ahead of its time, featuring a mutli-ethnic crew and exploring a lot of then current social issues. Unlike later Treks, which were more ensemble shows, TOS usually focused on the characters of Kirk, Spock and McCoy. Though it lasted only 3 seasons, it was never forgotten.
Season 1 (1966-1967)
Quick overview: The show was still finding its legs, but it had a lot of good episodes.
Best: Space Seed. This is the orignal episode to feature the villain Khan Noonien Singh, and has had more follow-up than any other single episode. In this initial appearance, the Enterprise crew finds Khan's ship containing him and his fellow "supermen" in suspended animation. Khan attempts to take over the ship due to his megalomania and Kirk stops him. Unlike Star Trek II, Khan isn't personally opposed to Kirk, as the things that caused his titular Wrath were the result of this episode. As a sidenote: Even though Khan recognizes Chekov early in Star Trek II, Chekov does not appear in this episode, as he debuted in Season 2. Honorable mention: The Enemy Within, Balance of Terror, Shore Leave, The City on the Edge of Forever.
Worst: Miri. This was a hard choice as Season One is pretty high quality and this is still a very watchable episode. On an alien planet that for some reason looks exactly like Earth (never followed up on, outside of the novels), a weird plague has killed all the adults, but made the children age very very slowly until they become adults and then die at about age 300.
Season 2 (1967-1968):
Quick overview: Largely considered to be the best season of the show. Walter Koenig rounded out the regular series as Pavel Chekov after Gene Roddenberry decided that he wanted to show a Russian character cooperating with the rest of the crew.
Best: The Trouble with Tribbles. As this season is considered TOS' apex, it's really hard to make a choice here, but I have a real soft spot for this episode. The genre of the series shifts to comedy with everyone still staying absolutely in character. It was revisited in DS9, and that episode will probably get mentioned in this series too. Honorable mention: Amok Time, Mirror, Mirror, I, Mudd, Journey to Babel
Worst: Catspaw: An episode specifically written for Halloween. The Enterprise is lured to a planet with two magic using beings. It just really doesn't fit into the sci fi of the rest of the show for me. It's still pretty watchable.
Season 3 (1968-1969):
Quick overview: For various reasons covered in depth elsewhere, the show went into a heavy decline with scripts being made that were actually rejected in earlier seasons.
Best: The Enterprise Incident: Kirk seemingly goes crazy and orders the Enterprise to deliberately go into the Romulan Neutral Zone, then Spock supposedly kills him. Just as you're wondering what's going on, the truth dawns: This is all a plot for the Enterprise to steal a Romulan cloaking device. Although this would be very useful in future episodes, Gene Roddenberry decided that invisible ships are boring and we wouldn't see the Federation regularly cloak until DS9. Honorable Mention: For the World is Hollow and I Have Touched the Sky, The Tholian Web, Let That Be Your Last Battlefield, Day of the Dove
Worst: Spock's Brain: An alien woman shows up on the Enterprise, knocks out the crew, and removes Spock's brain from his body to serve as the computer of their planet. This episode is basically a benchmark of bad sci-fi. Dishonorable Mention: Plato's Stepchildren (historically important because it's arguably the first interracial kiss in television history, but a BAD episode overall.)
TOS Best: The Trouble with Tribbles
TOS Worst: Spock's Brain
STAR TREK: THE ANIMATED SERIES (1973-1974) (note: Season 2 of TAS was 6 episodes, so I will combine the two seasons below)
Quick overview: The first response to the demand for new Trek. Most of the main cast was brought back, with Majel Barrett (Nurse Christine Chapel and other roles) and James Doohan (Montgomery Scott) also providing many other voices. Walter Koenig was not hired for the project, but did direct an episode. Episodes generally weren't of the same quality as the live action ones, but there were some good ones.
For us fans who were teenagers when this started, The Motion Picture was great! In retrospect, it sucked as redo of one of the episodes from TOS
Best: Yesteryear: Gene Roddenberry once stated that only live action television episodes or movies counted as canon, but this episode he liked. When Spock and Kirk return from time traveling through the Guardian of Forever, no one remembers who Spock is except for Kirk, and there's an Andorian as first officer. Spock realizes that the "relative" that he remembers as saving his life when he was 7 was in fact him from the future, so he has to travel back in time to complete the cycle. Honorable Mention: Practical Joker, One of Our Planets is Missing, The Time-Trap, The Slaver Weapon
Worst: Bem: The Enterprise has an alien exchange officer who insists on being included in a landing party and basically causes all sorts of trouble to "learn about humanity". The episode is named after the alien in question, who is in turn named for a common sci-fi acronym: Bug Eyed Monster. Dishonorable Mention: The Magicks of Megas-Tu
CLASSIC MOVIES (1979, 1982, 1984, 1986, 1989, 1991):
Overview: Originally, the demand for Trek's return was going to result in a new series: "Star Trek: Phase II". After the success of Star Wars showed that people liked sci-fi movies, the pilot episode for the series was poorly adapted into Star Trek: The Motion Picture, which was not very good. However, Star Trek II was a much better movie, leading into II, III and IV composing a trilogy, with V set soon after. Star Trek VI ended up being the final performance of Nichelle Nichols as Uhura and George Takei as Sulu. Kirk, Scotty and Chekov appeared in Star Trek: Generations and McCoy, Scotty and Spock appeared in TNG, with Leonard Nimoy's Spock actually surviving into the reboot films.
Best: Star Trek II: The Wrath of Khan: Even though some of the effects have not aged well at all (a common problem with TOS Trek), this movie is classic. Had they known that there'd be another four after it, they likely would have saved it for last, as it's a perfect send off. Khan, now obsessed with revenge on Kirk to Ahab-esque proportions (a paradigm they flipped for First Contact) is just the perfect villain, and for the first time, Kirk has to deal with a loss he can't wriggle out of. It is too bad that Kirstie Alley wanted too much money, because I would have loved to see her continue as Saavik. It is a bit ironic that Leonard Nimoy wanted to be written out as Spock, and 30 years later, he's still playing the character, who survived through TNG/DS9/Voyager time and even into the reboot universe (which we won't cover here as it's only two movies at this point). Honorable Mention: Star Trek IV.
Worst: Star Trek V. This movie suffered from a lot of issues, including a writer's strike, cuts that hurt the flow of the story, bad effects (note the scene where Spock uses his rocket boots to help McCoy and Kirk escape Sybok's men. Not only does the Enterprise have way too many decks, but they pass the same one twice.) The story is just weird too... Spock's heretofore unknown half-brother wants to find God at the center of the galaxy, which turns out instead to be some demon thing. Dishonorable Mention: Star Trek: The Motion Picture.
Next time, we'll hit the first four seasons of TNG.