Towards the end of "One Short Day," when Glinda sings, "Two best friends," you can hear a little chime that matches "ev'ry little trait" from "What Is This Feeling?", calling back to their initial relationship and how it had changed.
The foreshadowing for Fiyero's fate is clear once you pay careful attention to his name. The first two syllables "Fiyer-" sound like "Fear", somewhat synonymous with "Scare". And the "-O" rhymes with "Crow". Put those two together and what do you have? "Scarecrow"! Also the fact he repeatedly mentions being “brainless”...
It's little wonder Nessa grows to resent Elphaba years later, not just because she used her powers to help animals instead of her own sister. It's also because Elphaba flies. That's certainly a step-up from walking. And that only serves to add insult to injury to Nessa's bitterness towards her wheelchair-bound state.
Over the course of the musical, various phrases involving the word "good" are used — "making good", "thank goodness", "for goodness' sake", etc. — and as these phrases are overused by characters who are anything but "good", the word gradually loses all meaning . . . until the end, when the song "For Good" uses it with a different definition from the rest of the show, and it becomes meaningful once again.
What's more, when the finale tries to sing the last lyrics of "For Good" ("I have been changed..."), it's swapped with the lyric "No one mourns the WICKED!!" Put it together, and the last lines of the musical are "I have been changed for wicked." In a fitting roundabout way, it makes an ironic point that Glinda and Elphaba being changed "for WICKED" makes them more good than the phonies who were publicly deemed 'good' by Oz when really they hide dishonest interiors.
The: "You're beautiful." "Don't lie to me." "It's not a lie, it's just looking at something a different way." exchange that is repeated at the end doesn't only sum up Fiyero and Elphaba's relationship. It essentially sums up the main theme of the musical.
Elphaba makes several obvious prophetic statements in "The Wizard And I" ("Someday there'll be a celebration throughout all of Oz/That's all to do with me", "I'll be so happy I could melt", "When people see me they will scream"). However, she also makes a less obvious one at the end of "Defying Gravity": "And nobody in all of Oz/No Wizard that there is or was/Is ever gonna bring me down!" The person who ultimately brings Elphaba down (at least in the eyes of the public) is Dorothy, who is from Kansas and possesses no inherent magical abilities.
Glinda's line in "What is this Feeling?" in her letter to her parents states that "Of course, I'll rise above it" in regards to her current roommate situation with Elphaba. What makes this brilliant is that in the end, she must do this both literally and metaphorically. While in her bubble, she literally can "rise above" Elphaba. From a more symbolic standpoint, it describes how she must become the changing influence that Elphaba never could be (as described in "For Good") as she moves on from Elphie's "death"..
The Wicked Witch of the West's death scene in the original film, with the overwrought "Oh, what a world! What a world!" and all that, makes much more sense if you realize that Elphaba was deliberately being overdramatic to add weight to her faked death.
Two characters are referred to as "wonderful", the Wizard (his title, "The Wonderful Wizard of Oz" and Boq ("Oh, Boq, I think you're wonderful!" sung by Nessarose). Both lie about their true selves - the Wizard is only "wonderful" because the Ozians made him so, Boq is only "wonderful" in Nessa's eyes because Glinda manipulated him.
The final bridge of Defying Gravity (when Elphaba rises over the stage to scare the daylights out of the guards) opens with the lines "So if you care to find me, look to the western sky!" Not only is this a callback to Elphaba's eventual title "Wicked Witch of the West" but it's a clever use of foreshadowing. Where does the sun set? In the west. This is a sign of Elphaba's eventual fate and the fact her declaration of war are going to make things far worse for her.
In the musical, it's said that Nessarose's legs are non-functional because they're "all tangled up". In the MGM film, the Wicked Witch of the East's legs end up all tangled-looking after the ruby slippers appear on Dorothy's feet.
At the end of the musical, it is revealed that Elphaba and Fiyero faked their deaths. If we assume Elphaba's "melting" played out exactly the way it does in The Wizard of Oz, then it makes perfect sense. Elphaba set the Scarecrow on fire expressly to provoke Dorothy into throwing water to put it out, then purposefully stood where the water would splash her too, and the Scarecrow (actually Fiyero) was in on the plan all along.
In the MGM film, just before the Witch sets fire to the Scarecrow, she gives him a look. In the context of the MGM film, she's relishing the Cruel and Unusual Death she's about to inflict on the Scarecrow, but in the context of the musical, Elphaba is giving Fiyero a look that says "well, this is it", while trying to make it look as insidious as possible to sell the whole act to everyone else present.
When Glinda tells Elphaba's backstory in "No One Mourns The Wicked", at first it appears she's just retelling the basics of what she learned years ago from Elphaba, while the real audience are seeing the truth about Elphaba's conception. Come the final minutes of the show and it's revealed Glinda really was telling (or at least imagining) the full story; by now she knows the Wizard is really Elphaba's father and can make an educated guess as to how things happened.
The Wicked Witch of the East in L. Frank Baum's story, was the reason for the existence of the Tin Man, using her magic to keep him away from the woman he loved. Guess what happens between Nessa and Boq in "The Wicked Witch of the East" after he declares his love for Glinda?
The ending at first seems to just be a basic Writer Cop Out, having Elphie fake her death rather than die to give the ending more positivity, but it also works well to tie-in with one of the main themes of the story, that those in power will spread lies and spin facts to suit their narrative. In this case Elphaba's death, and the cause of it, are propaganda that serves as examples of these lies-from-those-in-power. The latter is something that was spread by Oz's regime as part of their 'she's Wicked' smear job, playing off of people's phobias towards her, while the former serves as a cover up story for Glinda's new regime to protect Elphie and bring peace. It ultimately just makes more sense for the show's narrative themes then it would to have simply killed her off, and still leaves the ending on a bittersweet note.
In the opening of the show, Glinda sings the lines "Let us rejoicify that goodness could subdue / The wicked workings of you-know-who! / Isn't it nice to know / That good will conquer evil?" Since everyone is rejoicing over Elphaba's death, the Emerald Citizens (and the audience) assume that the lines refer to the Witch of the West. But Glinda never names Elphaba at this moment...and she's just come from the Wizard's chamber, where she learned the truth about Oz and Madame Morrible. That's who the "you-know-who" is in the song: the two lying, scheming, would-be dictators who she just exposed. Glinda the Good quite literally subdued two truly wicked individuals! Sneaky.
When Elphaba casts a spell to save Fiyero's life in "No Good Deed", she declares "And however they try to destroy him/Let him never die/Let him never die!" In addition to making Fiyero indestructible, she also made him functionally immortal.
The sack that makes up the Scarecrow’s head might have came from Fiyero having that sack thrown onto his head and tied around the neck in an attempt to suffocate and/or blindfold him during his torture.
Elphaba's constant suffering under Fantastic Racism is nearly identical to a lot of real-life racism especially if you consider Elphaba's mixed-race status as the Wizard's illegitimate daughter (half-Ozian, half Earthian). The constant mocking of her green skin aside, her parents have no clue why she's like this, meaning Elphaba would be a throwback to a forgotten/unknown mixed-race ancestor (since they don't know her real father is the Wizard). Her father Frexspar can't stand looking at her and relegates her to be The Caretaker for Nessarose, her crippled but tragically beautiful sister, which was the fate of many historical mixed-race people who didn't pass. And then there's her extremely low self-esteem tied mainly to her skin color,which is true for a lot of minority girls and women.
Also, the above explains why Elphaba is so adamant to help the animals of Oz with her powers: she and them are both basically suffering the same kind of Fantastic Racism, but she has the ability to do something about it.
If Elphaba was even mocked for her green skin in college, just imagine how bad the bullying must have been in elementary through high school.
After "As Long As You're Mine," that loud shrieking sound Elphaba hears before she sees the house... Is that supposed to be Nessarose as she's dying? Either way, it's chilling.
Just how much did Dr. Dillamond remember after his speech was taken away?
Sorcery has enough of an intellectual foundation that they actually teach classes on it at Crage, yet somehow the field is still so underpopulated that when the Wizard needs talented mage types to help him rule Oz he sends Madame Morrible to a boarding school in order to act as his talent scout.
...Not to mention the fact that he seems to be scouting only at Crage Hall, which might indicate that none of the boys' schools teach sorcery. For some reason.
He was searching for amazing power and potential. If a person doesn't have power or potential (i.e. the Wizard) then all that education is useless. The potential has to be there first. The learning can come later. By searching for students with magical potential, they can find a powerful witch and have a degree of control over her. Don't know about the women thing... Females have babies and therefore have more life-force? Maybe cultural roles make men warriors and women magic-users?
Sorcery might have a decent foundation, but there aren't very many who are actually good at it—look at Glinda's professor, who is described as virtually incompetent. As for Madame Morrible being only at Crage Hall...maybe he has other scouts with the boys, but because none of the male characters study sorcery, they don't know.
Maguire showing his work again. In Baum's Oz books, magic wielders are overwhelmingly female. The best males can do is essentially alchemy, whipping up potions and pills. This is partly why Oscar Diggs was able to bluff his way into power; sorceresses and witches were fairly common, but a Wizard, not so much.
As "For Good" states, both Elphaba and Glinda have changed each other. Had it not been for that and the strength of their friendship, things would have gone much differently. Elphaba was used to being seen as an abomination, but it was knowing that Glinda was still on her side gave her hope that she could return once she had stopped the Wizards plan. Glinda was used to being well loved, and the character development from seeing how she was hurting Elphaba and could actually do something about it gave her the ability to work from the inside to fix the corruption. Had they not become friends, Elphaba's desire to be accepted would have made her capitulate to the Wizard's wishes from the beginning.