"The Crystal Empire": It had a great moral despite the story's botched portrayal. It was visually an amazing episode, especially for the point in the series in which it came out, and the Crystal Ponies and King Sombra served as an interesting emotional allegory. King Sombra himself was the most competent of the two-parter villains, going down fighting instead of on a "stand and gloat" moment, and setting a bunch of traps that really tested Twilight's prowess and showed how much progress she had made.
"Too Many Pinkie Pies": Pinkie Pie in an existential crisis is always interesting to watch ("Party of One" and "Pinkie Pride"). The idea had some very deep themes and was exploited very well for its comedic potential and as a character study. It gets better just talking about it.
"One Bad Apple": The song sequence was a very well-made pop homage and is catchy as all get-out.
"Magic Duel": Visually, a very unique episode. The epic setup had a lot of potential had the episode taken itself more seriously.
"Sleepless in Ponyville": Along with the following episode and "Hurricane Fluttershy", this showed Rainbow Dash's character development into a wiser, morally stronger potential mentor figure to Scootaloo. It was also Scootaloo's first focus episode, and the first in which Princess Luna shows up in a mentor role to one of the Crusaders, further developing her role as the reformed former villain trying to steer others away from going down the same path that got her banished.
"Wonderbolts Academy": Like the preceding episode, it really showed how far Rainbow Dash had come in her character development. Like "The Crystal Empire", it also showed how far she had come in her special talent; her skill in flying. The combination of both led to her setting a good example to the rest of the Academy and the Wonderbolts themselves just as she had to Scootaloo and Fluttershy previously, a top-notch show of her character development. The tough decision Rainbow Dash had to make would have made this a better key episode for Rainbow Dash than "Rainbow Falls" had the episode been pushed back to Season 4, if there would have been any knowledge of the key arc during Season 3's production.
"Apple Family Reunion": Great to see Applejack's first song and more of the Apple Family.
"Spike at Your Service": The first implementation of 3D CGI in the show. Although it did look awkward and stuck out as 3D effects usually do in 2D animated TV cartoons, the fact that they tried it shows just how much this show was willing to push the technical boundaries of what they have previously done and the perceived limitations of Flash-animated cartoons, and paved the way for a more seamless integration in "Princess Twilight Sparkle".
"Keep Calm and Flutter On": Discord absolutely owns the episode with his trademark quirkiness and scene-stealing charisma provided by Polsky's script and John de Lancie's always amazing voice performances.
"Just for Sidekicks": Really, I've got nothing for this episode alone. It doesn't really hold up on its own merits. The idea of setting it concurrently with "Games Ponies Play" was a great one, but unfortunately neither episode holds up well, alone or combined, as a particularly good episode of this show. This one doesn't hold up as particularly bad, either. If I really had to force myself, I'd say that it was nice to see the pets, even if they were all being jerks to Spike.
"Games Ponies Play": Even if the episode was totally lacking in the story department, a lot of the comedy was actually pretty well-timed and worked as much as you possibly could in such a plot. However, it just seemed more fitting of a show whose domain was straight-up comedy, not known for the character-driven narratives MLP is known for.
"Magical Mystery Cure": Most of the songs and the visuals of the second and third acts were top-tier for this show when this episode came out, and may continue to be into the fifth season. Although the Twilicorn transformation continues to be a mixed bag, the fact that it was done in the first place was an immense risk for the show to take. This episode executed the atmosphere and emotional weight surrounding the event exceptionally well, and I felt a bit better about it just looking at it for what it was -- the culmination and payoff of all of Twilight's activities from the previous episodes.