In no order: Next to Normal, Bridges, Spring Awakening, Fun Home, In The Heights, Wicked, Book of Mormon, Here Lies Love,Caroline or Change, and Matilda.
I included a couple of "revivals" that received their Broadway premieres and those that may not be "original" scores, but they are among my favorites, nonetheless.
The Wild Party (LaChiusa) The Full Monty Seussical Jane Eyre Urinetown Hairspray Wicked Bombay Dreams Caroline, or Change The Light in the Piazza Chitty Chitty Bang Bang The 25th Annual Putnam County Spelling Bee The Drowsy Chaperone High Fidelity Legally Blonde In the Heights Billy Elliot Next to Normal American Idiot The Scottsboro Boys Women on the Verge of a Nervous Breakdown Bonnie and Clyde Once Bring It On Matilda A Gentleman's Guide to Love and Murder The Bridges of Madison County Violet Hedwig and the Angry Inch
And though I haven't seen or heard them yet, I suspect Fun Home and Hamilton will be added to the list.
"What can you expect from a bunch of seitan worshippers?" - Reginald Tresilian
Great Comet of 1912 Book of Mormon Grey Gardens Fun Home Caroline, or Change Avenue Q Bloody Bloody Andrew Jackson [title of show] Ghost Quartet Urinetown Hairspray Here Lies Love Next to Normal 25th Annual Putnam County Spelling Bee
"...everyone finally shut up, and the audience could enjoy the beginning of the Anatevka Pogram in peace."
Even though it was deemed ineligible for the Tony, American Idiot is my #1 choice. High on my list are Hedwig, Spring Awakening, Passing Strange, The Last Ship and (in advance) Hamilton.
Fantod, the two albums from which the musical derive are both iconic, so you get no argument from me about that, but I believe "score" is properly based on the material, not the performances. I'd also note that Tom Kitt's work on the score was superlative-so much so that Green Day hired him to work on some of the arrangements on their subsequent albums.
Chaplin (the entire score is great, but the songs that really get to me are "What Only Love Can See", its Reprise, "Look at all the People", and "Man of All Countries")
American Idiot (I've been a Green Day fan since the late 90s, but what Tom Kitt and Michael Meyer managed to do with the band's American Idiot album and certain other songs from their catalog in adapting them into the theatrical format was nothing short of brilliant and, in some cases, made what were already superb songs - such as "21 Guns", "American Idiot", "Holiday", "Are We The Waiting", and "Boulevard of Broken Dreams" - even better)
Newsies (I heard the score for the theatrical version of this show long before I saw the film upon which it was based, and actually prefer the theatrical version of the score to the original film's, especially since the stage version has songs like "Something to Believe In", a much better version of "Santa Fe" that makes far more sense story-wise, "Watch What Happens" and its Reprise, and a much more bombastic version of "Once and For All")
The Little Mermaid (Although the 1989 film's score remains in my mind one of the best film scores of all time, the score for its musical adaptation comes very close to surpassing it, especially with songs like "I Want the Good Times Back", "One Step Closer", and the Quartet version of "If Only", all of which really take what was already a great core storyline and enhance it)
The Producers (I saw the filmic adaptation of the musical before hearing the Original Broadway Cast recording, and while both are great in their own right, I prefer certain aspects of the film's score to its theatrical counterpart, particularly the orchestration on "When You've Got It, Flaunt It" and "Along Came Bialy")
This is a tough one. Definitely i would say The Light in the Piazza for sure (what a beautiful score just beautiful), Next to Normal, If/Then (just love it), Heathers (fun some good songs), Grey Gardens (exquisite), Far From Heaven (I haven't seen it but the cast album is beautiful) Bridges of Madison County (I mean come on one of the best scores written in a long time), Natasha, Pierre, and the Great Comet of 1812 ( I made myself sit through the whole cast album and wow just an amazing and beautiful piece of theatre), The Visit (just a good score all around), Fun Home, Caroline, or Change (just as good as FH), Rebecca, Finding Neverland (the Frankel and Korie score, their might have been some problems but they had some beautiful material),Wonderland (It's a fun score), Women on The Verge of a Nervous Breakdown (I haven't listened to all of it but I love every song I have heard. Invisible is such a great modern piece), The Last Ship. That's all I can think of.
Bring It On (I've never seen the movie, but really liked the music for this one; it reminded me of stuff like Grease and the High School Musical Trilogy; Lin-Manuel Miranda, Tom Kitt, and Amanda Green really scored, no pun intended, with this one, with songs like "What I Was Born to Do", "Bring It On", "It's All Happening", "Enjoy the Trip", and "We're Not Done" really standing out)
Spring Awakening (This show strikes me as being what you'd get if you took Les Miserables, American Idiot, RENT, Eve 6's Showerhead, and The Offspring's Kristy, Are You Doing Okay, The Kids Aren't All Right, and Gone Away and threw them into a blender with the plotline from J.K. Rowling's novel The Casual Vacancy. Duncan Sheik's musical score is great, and pairs perfectly with Steven Sater's lyrics, which are at their most poignant and powerful on songs like "Mama Who Bore Me", "The Dark I Know Well", "The Mirror-Blue Night", "The Guilty Ones", "Those You've Known", and "The Song of Purple Summer")
The Wedding Singer (The Wedding Singer was the film that completely changed my opinion on Adam Sandler and helped me appreciate just how brilliant of an actor and comedian he is and was, and the spirit of the original film very much lives on through the score of its musical adaptation. I'm particularly fond of the songs "It's Your Wedding Day", "Someday", "A Note From Linda", "Somebody Kill Me", "Casualty of Love", "Come Out of the Dumpster", and "Grow Old With You")
Tarzan (I love the animated version of this show, but really like what was done, for the most part, in adapting it to the stage [I don't get why they changed Terk's gender, but that's my only complaint about the show]. The new songs that Phil Collins wrote are excellent, particularly "As Sure as Sun Turns to Moon", "Different", and "For the First Time", and fit perfectly into the original storyline)
Fun Home (Who would've thought that a graphic novel memoir written in 2006 would turn out to be such a perfect fit for the stage? Jean Tesori and Lisa Kron, that's who. These two really knocked it out of the park on this score, with songs like "It All Comes Back", "Welcome to Our House on Maple Avenue", "Changing My Major", "Ring of Keys", "Days and Days", "Telephone Wire", and "Flying Away" standing out in particular)