I thought I'd classify my favorite episodes in general categories, to show what qualities I value in the show so far. Feel free to respond with your own ideas, ratings, and responses!
INCREDIBLE
Griffon the Brush-Off - The development of friendship between Pinkie Pie & Rainbow Dash really shines, and Gilda stands out as an understandable villain. The pacing is like music.
Bridle Gossip - Here a shifting spotlight of character focus, character-driven comedy, and a steadily paced view of Twilight's increasing doubts about Zecora combine to make this a beautiful demonstration of what the show can do if it tries.
Suited for Success - This is the episode that really made me like Rarity's character. Artistic qualities & generosity are shown, not told. The peripheral characters' reactions feel genuine and understandable.
Feeling Pinkie Keen - Despite the disarming moral (which makes sense after a bit of logical interpretation), the 'classic' cartoon-y quality & the various peripheral character reactions to 'Pinkie Sense' make this a personal favorite.
Green Isn't Your Color - Perhaps my favorite episode, this one moves swiftly along with a cosmic giddiness unmitigated by the very palpable tension balanced between Fluttershy, Twilight, and Rarity, and wonderfully present in all of Pinkie's memorably off-the-wall appearances. Each scene is a gem.
Party of One - Can you tell I'm a Pinkie fan? This episode was perfect for me -- Pinkie is at once empathetic & hilarious. The supporting cast shine as well, and the opening song is one of my favorites; the pacing is immaculate, and the final breakdown feels authentic despite its intrinsic bizarreness.
GREAT
The Ticket Master - This is the first episode that really inspired me to become a fan -- it set the bar high, but later episodes are even better. The first insight we get into actual Ponyville life, we really feel Twilight's struggle develop, and we are genuinely happy when it works out in the end.
Applebuck Season - In this first "character episode," we see not only Applejack's story but the way it affects her friends; each pony feels important to the motion, and the jokes aren't half-bad either, based as they are in a feeling of empathy with characters.
Swarm of the Century - For me a quasi-'sequel' to Bridle Gossip, this episode demonstrates excellent balance between characters. The main characters' attempts to solve the problem are spiced up nicely with Pinkie's intermittent appearances.
Sonic Rainboom - With a very casual pace, and excellent Fluttershy & Rainbow Dash moments -- not to mention Rarity -- this one easily ranks quite high for me. Seeing Clousdale is also a treat!
Stare Master - The first 'CMC' episode with all three in action, it is successful largely because of the addition of Fluttershy to the equation, balancing the Cutie Mark Crusader's jiggery-pokery. There are some great moments throughout this one, perfectly presenting the situation.
The Best Night Ever - One couldn't ask for a better or more fitting season finale; heck, it's so strong it could even be a SERIES finale! Each pony's story arc feels just as fresh and sympathetic as the beginning of the series, and a brilliant counterpoint to the equally good bookend that is "The Ticket Master." Celestia has another great role to play here as well. And of course, Fluttershy's performance steals the show.
Luna Eclipsed - The only Season 2 episode to reach this status for me 'feels' like it was written very early in the process, ie, in a 'Season 1' vein. For instance, despite Twilight's deposition as 'main character' in "Lesson Zero" (an act that understandably frees the writers up, but which ultimately resulted in carelessness), she still stars here like nothing has happened. Luna's character is wonderfully balanced, and Twilight's character regains her interest. Pip is initially irritating, but eventually fulfills his cutesy roll quite admirably. Other possible negative qualities (such as Zecora's slightly embarrassing return and a lack of 'classic' ensemble moments) are nicely mitigated by positive performances in the focus cast.
GOOD
Friendship is Magic Part One - As the first episode in the series & the first one I ever watched, I was understandably skeptical. But the character introductions establish things in a nicely endearing way, and you can really feel the sense of discovery; Twilight's character was instantly empathetic for me, and that real feeling is what kept me watching.
Friendship is Magic Part Two - A truly nice resolution, if a bit stuffy in structure -- these first two episodes feel like a lovingly-constructed bridge between older MLP tradition and Faust's new realizations.
Boast Busters - A very well-done episode, but it never really did a whole lot for me. Trixie is a fun character, while Snips & Snails are (intentionally) irritating. Wonderfully structured, it misses for me a special "something" to make it great. But the feel of care remains woven into its creation, and so feels 'classic.'
Look Before You Sleep - An excellent tri-character study, Twilight's doofy demeanor nicely plays off of Rarity and Applejack's personality conflict. Fun in an endearing way, for me, and the entertainment is mostly generated from subtle gestures that make the characters identifiable and relevant.
Dragonshy - A great 'adventure' episode with an all-star cast. Fluttershy's moment at the end remains a watershed. Classic in every sense, with a fine sense of balance.
Winter Wrap-Up - The song in the center was initially off-putting for me, but eventually became a highlight after re-watching. This episode seems to embody "the norm" for FIM, seeming very central in many different ways for the first season at large.
Call of the Cutie - As the first 'CMC' episode, I really enjoy this. The plot motion is paced just right, and the writing is confident with nothing to prove; it's a solid episode, and a refreshing change of scenery.
Fall Weather Friends - Another solid episode, with great peripheral character motion surrounding the essential Rainbow Dash / Applejack dynamic.
Over a Barrel - A somewhat problematic ending & stereotyped racial portrayals don't stop this from being a very fun episode. The conversation in the train at the beginning remains one of my favorite scenes of the series.
A Bird in the Hoof - A very fun Fluttershy episode (it's very difficult to write bad Fluttershy dialogue, just as it's very difficult to write GOOD Pinkie Pie dialogue... and Pinkie's my favorite pony!). Celestia's character really stands out here, cheerfully reminding me of Dumbledore, and feeling that all's right with the world. Fluttershy's moments with Philomena are in a wonderful 'classic' cartoon-y style, though the chase scene could be a bit much.
The Cutie Mark Chronicles - The CMC grate a bit here, but they are more than well-met with the rest of the cast's fun flashback stories, each of which is endearing in its own way. A sickeningly cheese ending is saved by the Scootaloo.
Owl's Well that Ends Well - Despite my distaste for the Owl, Spike's performance is quite nice, and the hilltop meteor shower is magical. Not a personal favorite, but there are no real problems beyond that.
The Return of Harmony Part One - The pacing is pretty compressed, but that's understandable. Celestia is pretty uptight, but that's understandable. The ponies each have their moments, but there's a real feeling of 'cramming it in', and some characters -- especially Pinkie & Applejack -- are shortchanged. Despite this, Discord is a masterful villain, the best in the series so far.
The Return of Harmony Part Two - Things improve quite a bit here, but portions still feel hurried and unnatural. Pros include the truly affecting negative performance of the greyed-out ponies, Twilight's starring role, the goofy Star Wars ending, and the incredible zaniness of Discord's vision. A real blemish, however, is the heavy-handed volte-face Twilight undergoes when she re-reads her old Friendship Reports; while this is a wonderful & fitting concept, the execution left me feeling a tad alienated.
May the Best Pet Win - Tragically following in the tradition of a largely 'rubber' supporting cast in season 2, this episode is saved by some fun Rainbow Dash moments, a fun song, and some endearing Fluttershy commentary. Entertaining, but most of the three-dimensional magic 'interactions between friends' of the first season seems largely absent.
OKAY
The Show Stoppers - The first episode that I really didn't like, for a few reasons: the Cutie Mark Crusaders don't have any real balancing force to distribute the focus; any appearances of the main cast feel hollow & rubber; and the ending song is truly cringe-worthy. I've since come to terms with most of these factors, since the song is actually kind of fun, and the scene with the Crusaders preparing their act is pretty classic. The hollowness of the supporting cast remains a problem for me.
A Dog and Pony Show - Again, the supporting cast doesn't have much to contribute to this Spike-and-Rarity story. The Diamond Dogs are entertaining, and Rarity's scenes are genuinely funny, but the ending moral remains a small issue -- and Spike's romantic fantasy didn't do much for me. The most damage, however, results from the complete thoughtlessness in the writing for the peripheral cast.
Sisterhooves Social - The first Twilight-less episode, this was a pretty ambivalent experience for me; there's nothing really WRONG with it, but throughout it feels like something important is missing. Applejack's performance is feebly one-dimensional, and other characters don't fare a whole lot better. Granny Smith's goofy monologue is a highlight, but the comedy is cheap & mitigated by a lack of inspired character-driven writing. Probably the worst thing about this one is that it is neither GOOD nor BAD; it's just not very interesting at all, despite some 'touching' moments towards the end. Tabitha St. Germain's voice acting saves this from being absolutely pedestrian.
The Cutie Pox - More engaging than the last episode, it suffers nonetheless from a one-dimensional character focus (solely on Apple Bloom), a lack of inspired peripheral roles -- the adult ponies again feel rather 'rubber' -- and yet another grating return of Zecora, whose presence feels less like a real character and more like a cheap plot device than ever. It's okay, but it's missing any of the qualities that keep me watching the show.
The Mysterious Mare-Do-Well - Another single-pony plot with virtually no subsidiary character focus. Rainbow Dash's experience is not anything I can identify with; it feels like she's being 'forced' into her role; basically the writing is not smooth, and the performances don't make me care. Despite this, the visuals are more engaging & fluid than ever, with a variety of locations explored (some rather dubious and ill-fitting with earlier depictions of Ponyville). Ashleigh Ball's voice acting becomes positively grating by the end, sounding like she's worn out her voice, and understandably so -- barely any pony other than Rainbow has anything to say!
AWFUL
Lesson Zero - Rarely have I been so depressed by a single 20-minute television spot. Sympathetic characters go out the window -- Twilight, who I empathized with so strongly 28 episodes prior, is a grotesque caricature of her most basic surface qualities; the other ponies feel utterly inorganic and one-dimensional, like rubber dolls. The pacing is offensively scattered, and even the jokes -- the undeniable focus of the whole production -- just don't cut it, being based in cheap visual gags rather than identifiable character-driven humor. (Possibly on the plus side, the visual style and cinematic presentation are much more 'advanced', with a wider variety of angles & nuanced animation... although this could be something further alienating. And the 'new' intro is downright nauseating, the 'update' rather cruelly pointless.)
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For me a good MLP episode is like music: a foreground, a middleground, and a background, with audience attention shifting smoothly between. In music, this is developed by focal melodies, counterpoint, harmonic cushions, rhythmic underpinning, and so on; in MLP, this is achieved by playing characters off each other, with strong leading roles supported by an interesting supplementary cast (not to mention pacing, visuals, audio, etc.). The most successful episodes for me form a believable flow from character to character, empathy forming the most important factor in any individual character's appeal, with humor derived from an affecting 'relationship' between the viewer and the character -- in this way, jokes appear unique and meaningful, rather than coarse, cheaply global, and context-irrelevant.