Falsettoland is my favorite musical, specifically “Unlikely Lovers” and “What Would I Do?”. I cry everytime. Course, it may be because my younger gay brother played the part of Whizzer when he was in college, and seeing him portray the part of a man dying of AIDS was really rough.
Once on This Island also has a really great ending, when the Gods are bringing Ti Moune to them.
My favorite moment from RENT has to be Gordon’s speech during Life Support.
“I’m a New Yorker, fear’s my life”
For pure fun, I’d have to go with “If I Were a Rich Man” from Fiddler on the Roof.
I also love “Just You Wait” and “Get Me To The Church On Time” from My Fair Lady.
“Sancho! My ARMOR!”
The end of Pippin.
When the painting is finished (both times!) in Sunday in the Park with George.
Into the Woods:
“Would you like a blind girl instead?”
“AAAAAH!” “How dare you!”
“Put them out of their misery!”
“We’re not that miserable!”
The part at the beginning of Rent when Collins is on the phone, telling Mark and Roger to “Throw down the key,” I caught it! (I had to give it back, but they gave me a guitar pick – and the candle!)
When The Scarlet Pimpernel came through town, the touring company had several of the original Broadway cast in it. The man playing Percy/the Scarlet Pimpernel would take opportunities to ad-lib. The second time I saw the show, he actually had other cast members forgetting their cues in their efforts not to break character.
My favorite moments from that show are “Into the Fire,” where Percy recruits his fellow noblemen to fight against the atrocities of the French regime, and “Creation of Man,” where the League goes all “frou-frou” to throw the Prince of Wales off their trail.
My favourite moments are any time Linda Eder opens her mouth to sing, particularly if she’s singing ‘Someone Like You’ from Jekyll & Hyde. She’s the greatest singer in the world.
My other favourite moments would be when any piece of musical theatre by Stephen Sondheim finally ends. Contemporary genius / living legend / massive worldwide following / yadda yadda yadda… I don’t care. I’d rather stick spikes in my ears, it’s less painful.
I second NoCoolUserName’s nomination: “Sancho! My armor! My sword!” Chills every time.
“The rain in Spain stays mainly in the plain.” According to legend, the first time Julie Andrews spoke this line “correctly”, there were audible gasps of relief from the audience.
Virtually all of 1776.
“I’ll go home with bonnie Jean” from Brigadoon.
The Lion King. At the very beginning, when the sun on the scrim curtain rises as Rafiki chants the Swahili opening to “Circle of Life” while the chorus from the wings echoes the chant, then the animals walk down the aisles past the audience–so much more impressive than the movie.
Little Shop of Horrors. When the vines drop on the audience during “Don’t Feed the Plants.”
Carol Burnett’s skirt falling down at the opening of the second act of Putting It Together.
Also the only musical I’ve been to that I wasn’t in.
My personal favorite part (at the moment. I’m sure it’ll change, oh, tomorrow 
) is Raoul’s part in “Point of No Return”:
I love her! / Does that mean nothing? / I love her! <…> Christine, forgive me, please forgive me… / I did it all for you, and all for nothing… <…> I fought so hard to free you…
Les Miserables has so many great moments, it’s hard to pick my favorites, but here goes:
Ditto on Javert’s suicide, Eponine’s death, and “Who Am I?”(the courtroom scene where Valjean reveals his true identity).
When Marius sings “Empty Chairs at Empty Tables” and the ghosts of all his friends appear around him. I cry like a baby every time.
The end of the prologue, when Valjean is given a second chance at freedom:
I’ll escape now, from that world
From the world of Jean Valjean
Jean Valjean is nothing now!
Another story must begin!
Hard to describe that moment if you’ve never seen it, but it’s incredibly powerful.
There’s probably some I’m forgetting, but I’ve not seen it for a couple of years now.
Moving on to The Phantom of the Opera, aka my favorite show of all time:
The chandelier going up during the overture. Gives me chills.
Christine going through the mirror after the Phantom appears in it.
Music of the Night. I think the best version I’ve ever seen was by Ted Keegan as the Phantom. Dear lord, that man has a voice.
Masquerade. Great number, great scene.
“Wishing You Were Somehow Here Again”
The end of “Point of No Return” when Christine realizes she’s onstage with the Phantom(who killed her co star and came onstage in his place).
When Christine kisses the Phantom:
Pitiful creature of darkness
What kind of life have you known?
God give me courage to show you
You are not alone!
Sad to say, I could type the libretto of Phantom entirely from memory and say that’s my favorite part, but I think I’ll just stop here. 
Cabaret, at the very end, the backdrop is a scrim curtain dressed as the wall of a concentration camp and the theatre is is flooded with the loud roar of the crematoria, we see the Emcee dressed as a prisoner wearing the yellow star of David and the pink triangle, singing, "Auf Weidersehen, A Bientot. . . " <drumroll, then lights out>
I was in tears.
Another Rent vote, though my moment, makes me bawl like a baby every time, is the curtain call. There’s a blatantly obvious gap in the line where Angel should be. And once the poignancy reaches critical mass, Angel comes out all in white to take his well deserved bow. The mournful “I’ll Cover You” is a close second.
And it really isn’t a relatable moment, because it was a version of Godspell that I stage-managed, but the director had tracked down a very cool beaten up yellow-diamond “No Entry” road sign, upon which Jesus was crucified. When he was cut down, the sign was removed as well. Chillingly symbolic, even for an unreligious fart like me.
The whole magic that theater should be comes out the instant Michael’s feet leave the floor in Peter Pan.
Judging from most of the posts here, some people need to get out and see a musical more often. I mean, come on: Les Mis? Miss Saigon? Rent? —the bottom of the barrel. Musicals for morons.
Thanks for posting, Nanook, you’ve added a lot to this thread. Since you evidently have seen much finer musicals than us mere mortals, why not share your favorite moments with us?
(Adds nanook to the list of people who hopefully can’t afford $5)
This is a fascinating discussion, everyone!
But a page and a half and no one’s mentioned West Side Story yet? Shameful! I see I’ll have to make up for it, which is easy since the whole musical is crammed with unforgettable moments:
Leonard Bernstein’s spectacular overture and the opening gang scrimmage, which transitions to “The Jets’ Song.” How can you not get shivvers of delight at such music?
The square, bland little community dance that goes awry, particularly the Jets/Sharks Mambo dance war with Anita and Bernardo squaring off against Riff and, uh, his somewhat bland girlfriend. All this segueing to the lovely moment when Maria and Tony first meet.
The Quintet reprise of “Tonight,” as the varied voices of Anita, Tony, Maria, Riff & the Jets, and Bernardo & the Sharks all blend together in thrilling anticipation of an eventful evening … of one kind or another. Cripes, Bernstein was a freakin’ genius.
The song everyone loves to snap to, “Cool.” Although I prefer the movie’s placement of the song to the stage musical’s. In the film, “Cool” is switched with “Officer Krupke” so that it takes place in the taut, angry and shocked aftermath of the rumble. (When seeing the stage version, I never quite buy “Officer Krupke” taking place after all hell’s broken loose and the Jets have lost their friend and leader. I love the song, it’s hilarious, but it just doesn’t fit there for me.)
Speaking of which, I’ve gotta give props to Stephen Sondheim’s snarky, hilarious lyrics for “Krupke” (as well as “America”). They’re his personal high points in WSS. The rest of his work for the show feels like, dare I say it, standard generic musical fare. (“Today, the world was just an address, a place for me to live in, no better than ‘all right’” indeed! I know he was running out of rhymes for “Tonight,” but c’mon! Quite a far cry from his later brilliance at finding clever and unexpected rhymes.)
When Maria learns of her brother Bernardo’s death. She goes from devout fearful prayer (‘Please make it not be true…’) to fury directed at the man she loves (‘Murderer!’) to despair as she collapses in Tony’s arms. Leading to …
“Somewhere.” Simply the most poignant, beautiful song I’ve ever heard.
The intense scene where Anita, mourning her boyfriend’s loss, figures out that Maria’s slept with his killer. Everything from her enraged “A Boy Like That,” to Maria’s gorgeous “I Have a Love…” counterpoint, and then their rapprochement when Officer Krupke arrives to interrogate Maria regarding the murder. Gotta admire Maria’s quick thinking in asking Anita to go to the drugstore for aspirin (she’s tacitly asking Anita to go warn Tony that she’ll be late for their meeting) and her cajones, considering Anita’s hatred for Tony!
When the Jets taunt Anita and assault her, all accompanied by a chaotic, mocking version of “America.”
And, of course, Maria’s final goodbye to Tony: “Te adoro, Anton…” Which is the cue for the exquisite finale, the instrumental conclusion of “Somewhere.” Oh, those heartbreaking, hopeful chords contrasting with the dark, foreboding single repeated low note … ! If there’s a dry eye in the house at this point, something is seriously fucked up in the production.
Believe it or not, I have seen other musicals too. 
Fave moments include:
[ul]
[li]Lady Thiang trying to convince Anna that the King is indeed “Something Wonderful” (tied with “Somewhere” as my ultimate favorite musical number – although Oscar Hammerstein II’s lyrics for “Something Wonderful” out-do Sondheim’s for “Somewhere.” [/li][li]Also from The King and I, the March of the Siamese Children. Man, Richard Rodgers was incredible. I’ll never cease to be amazed by the man’s skill and range, from the sophisticated, arch romanticism of his partnership with Lorenzo Hart to the emotional, thematic lushness of his Hammerstein years.[/li][li]The moment that changed musicals, the beginning of Oklahoma! – not with a huge overture or rousing choral number, but with Curly’s simple ode to cows, corn and meadows, “Oh, What a Beautiful Mornin’!” I also love the dark humor (unusual for Hammerstein) of “Pore Jud is Daid.” For a non-musical scene, there’s the tense auction scene as Curly and Jud compete for Laurey’s basket of goodies. So to speak.[/li][li]To make up for my earlier Sondheim-dissing, I must echo those citing Sweeney’s “Epiphany,” both for the music/lyrics and the powerful performers who play Sweeney (either Len Cariou or George Hearn will do!). And the hilarity of “A Little Priest.” And the creepiness of Judge Turpin’s self-flagellating masturbatory “Johanna.” And Toby’s anguished “Nothing’s Gonna Harm You.” And the chilling beauty of the different version of “Johanna” set against Todd’s calm dispatching of his ‘clients’. And OH the agonizing irony of the scene when we realize that the Barker family has at long last been reunited – and none of them knows it! As Sondheim wrote, “God, That’s Good!”[/li][li]“You’ve Got to Be Carefully Taught” from the otherwise ‘meh’ (for me) South Pacific. SP just isn’t one of my fave R&H musicals, but the anti-bigotry message of this sarcastic, bitter, self-aware song coming from Lt. Cable is a powerful one. (“You’ve got to be taught – before it’s too late, before you are six or seven or eight! – to hate all the people your relatives hate. You’ve got to be carefully taught…”) [/li][li]To save space, I’ll just cite all of Jesus Christ Superstar, but particularly the Overture, “This Jesus Must Die,” the rollicking “Herod’s Song” and Judas’s frenzied “Damned for All Time.”[/li][li]As long as I’m praising Andrew Lloyd Webber/Tim Rice, how’s about “A New Argentina,” the Act I finale of Evita? The musical chair game of “Art of the Possible” is a frighteningly accurate look at political machinations that sounds like the current Bush & Blair administration playbook: (“One always claims mistakes were planned; when risk is slight, one takes one’s stand … with much sleight of hand; Politics – the art of the possible!”)[/li][li]In 1776, one of many great moments is South Carolinian congressman Edward Rutledge’s acidic declaration of the anti-slavery northerners’ apparent hypocrisy in the song “Molasses, to Rum, to Slaves.” And John Adams’ remark to his colleagues: “I have come to the conclusion that one useless man is called a disgrace; that two are called a law firm; and that three or more become a congress.” Also, just about every line out of Benjamin Franklin’s mouth.[/li][li]Damn Yankees: The Devil (aka Mr. Applegate) sitting back and fondly remembering how “Those Were the Good Ol’ Days!” (“I’d sit on my rocking chair, [/li]so peacefully rocking there, counting my blessings by the score. The rack was in fashion, the plagues were my passion … each day held a new joy in store!”) Also "Whatever Lola Wants…,"Lola’s attempt to seduce Joe. I love how she alternates her seduction style back and forth from cutesy coy to brazen vamp. I was lucky enough to see Gwen Verdon and Ray Walston in a revival. Even though they were both kinda long in the tooth, they were magical.
[/ul]
Sorry for rambling … oy I need to shut up. I’m a pushover for musicals!
At the end of Dick Latessa (as Wilbur Turnblad) and Harvey Fierstein’s (as Edna Turnblad) duet “Timeless to Me” in Hairspray :
(going by memory here)
Edna : You don’t look Jewish.
Wilbur : You can’t always tell.
Edna : (in her most husky, seductive voice) : Yes … you can.
Actually, WSS is my very favorite musical of all… I just haven’t seen it in ages, and know it mainly through the soundtrack. That said, I think the multi-part Tonight with the Jets, Sharks, Tony, Maria and Anita is absolutely brilliant, and is, musically, the best “showtune” ever written.
Anyone familiar with “The Last Five Years”? The first “meeting” of Jamie and Kathy
during “Next ten minutes” always gets to me. Also for ragtime, Sarah’s funeral is the most powerfull note i have seen an act 1 end with…“we’ll never get to heaven, till we reach that day”