Episode 26's theme song, "At the Gala", truly takes the cake. It's a song of triumph, not only for the Mane Cast, who have waited all year for this day, but also for the fans who stuck with all 26 episodes and found each of them awesome. Rainbow Dash's rock segment is arguably the crowner of the entire song, too. It's also based off the song "Ever After" from Into The Woods, and they match up so well too.
Find A Pet, where Fluttershy and Rainbow Dash sing when trying to pick a pet for Rainbow Dash in "May the Best Pet Win!" (the first song of the season!) is a perfect blend of awesome, cute, and funny.
Being able to work in not just a few recognizable measures but a large bulk of "Ride of the Valkyries" is pretty impressive as well.
The featured singers in this song were Sweetie Belle and Apple Bloom. What makes this impressive is that both parts are sung by the same actress - an 11 year old girl.note That would be the very talented Michelle Creber. She's obviously not so young anymore, but it's known that she was 10 when she sang Sweetie Belle's first song, "Hush Now, Quiet Now". Since this song came almost exactly a year later, well... Incidentally, Sweetie Belle's regular VA, Claire Corlett, did not sing until Season 4. In Season 3 we find out why.
The Japanese version also manages to generate a high quality dub that can be considered to be on par with the original.
Twilight finally sings a solo (MORE THAN ONCE!) in the second season finale, and it is glorious.
Her "B.B.B.F.F" song is both beautiful and heartwrenching, especially if the person listening has any siblings that they've grown apart from. And that's just the first rendition; try to contain your feels when she sings its reprise.
Special mention has to go the harmony on the very last "forever" in the first song. Bonus points for Daniel Ingram confirming that Twilight's glissando deliberately matches the first few notes in the theme song.
From "The Crystal Empire - Part 1", there are two songs. The first is "The Failure Song". It gives us a sincere and heartfelt song with impressive visuals that demonstrate an upgrade to the show's animation quality. As well as that, we have a few funny moments, as well as hearing Spike sing for the first time.
And now, composer Daniel Ingram has released a collaborative rock remix of the song.
Within about a week, at least 21 remixes of the song could be found. It is just that catchy.
From "Apple Family Reunion" comes the beautiful song "Raise This Barn". Not only is it better than most country songs today and especially the first time we've heard Applejack really sing since "The Best Night Ever",note Unless you count Hub promos but it's also captures the true spirit of the Apple Family down to the capital A. Not a bad song to raise barns and/or set everything right to.
"I've Got to Find a Way" a tragic, yet beautiful song depicting how messed up everything is with the Mane 6's destinies switched.
"A True, True Friend", which helps exemplify what the Mane 6's friendship is all about. Words fail to describe how spine-chillingly epic and uplifting the song is, especially as it shows each of Twilight's friends rediscovering their true selves; it even replaces the title theme for the end credits.
"Celestia's Ballad", which features for the first time Celestia singing. And it's beautiful. Throw in the sheer nostalgia and emotional impact this song employs and you'll be shedding liquid pride for hours.
"Bats!" has the episode's title song, and it's simply divine! Taking inspiration from The Nightmare Before Christmas, and the song "Savages" from Pocahontas, it displays Applejack and Fluttershy's reasoning towards how the vampire fruit bats are vermin and how the vampire fruit bats are just like every other pony respectively. Not only do its visuals show off how contrary both sides are to the story, but its grand finale amplifies how grand it really is to listen to.
Gilda's Threat. In the words of one of the commenters on the video: "This reminds of some of the music from RA3".
The music that plays during the celebration at the end of the first two episodes.
The BGM that plays during Applejack's corruption in the Grove of Truth is a masterpiece of Danny Elfman-style creepiness.
The music that plays all through Applejack's restoration, from around :38 to 1:00, especially when it shows her memory of running alongside Rainbow Dash. In fact, all the music during the restoration of the elements kind of makes you wish there was a trope page for Crowning Music of Heartwarming.
The BGM that plays from 17:00 to 18:00 in "Lesson Zero", when the entire town of Ponyville is fighting over Smarty Pants, is incredible. It's creepy, discordant, and surprisingly grandiose...befitting the climax of the episode and the height of Twilight's craziness.
The music cues when Rainbow Dash is finally bored enough to try reading from "Read It and Weep" borrow heavily from The Neverending Story when Bastian is about to open the book for the first time.
Something very similar to "The Lonely Man" (aka the "David Banner hitch-hiking" theme) from the 70s The Incredible Hulk TV show appears in Putting Your Hoof Down when Fluttershy realizes she's lost control, and slowly walks back to her cottage, to isolate herself from other ponies while she tries to fight the monster within.
The background music during the "hoovicure" scene during "Ponyville Confidential" Is a particularly subtle example. It's quiet and tense ambient music that you wouldn't otherwise notice. What makes it awesome is that it takes a scene that should be lighthearted and funny, and turns it oddly dark. It conflicts with each pony's musical cues, evoking the idea that everypony knows the gossip is wrong, but is ignoring those feelings.
Further from "Sleepless" the BG music cues when Rainbow Dash is telling Scootaloo about being scared, and at the scene at the waterfalls, borrows from "No One Is Alone" from the Sondheim musical Into the Woods (a very appropriate song here).
One of the ways the music in this episode is used so well is that Plot A - the swapped cutie marks - is set up, dramatized, and resolved through three separate songs with just a handful of spoken scenes. Compared to musical attempts that most television shows try to do (even in Friendship Is Magic, such as "The Success/Failure Song" from "The Crystal Empire") where it reiterates plot points just made, this episode used the songs very economically for plot development instead of just exposition. That's partially why both Daniel Ingram and M.A. Larson are credited with lyrics for this - they needed to work hand in hand to make this happen.
"A True True Friend", the highlight of the episode, would not sound as musically awesome if it wasn't so tightly connected to the cutie mark-switching plot and the order which with they have to be resolved - there's almost no other way for that song to build up from a quiet duet between Twilight and Fluttershy, have an amazing bridge sung by Rarity, and end on a Crowd Song with Pinkie's return, if the cutie marks were swapped in any other fashion.
The music from the chorus is previewed when Twilight realizes what needs to be done to help her friends, and reprised when she figures out how to finish the original spell, which transitions to a dramatic musical climax as the Elements are activated.
Not to mention the gloriousness that is Nicole Oliver's singing voice.
In "Testing Testing 1 2 3", the backing music during the segment showing what the rest of the town was doing during the second Twilight/Rainbow flying sequence is wonderfully evocative, capturing the spirit of "It takes a village..." aid that the town provides to Rainbow.
In "Twilight's Kingdom - Part 2", we get not only the music heard during Twilight's battle with Tirek, but also the music heard during the Rainbow Power sequence, which is an epic rearrangement of the original My Little Pony jingle.
Alright, this is half-fan music, but this cover of "Jingle Bells" featuring Maddy Peters, the voice of Scootaloo, is pretty awesome.