CGCJ

Here's more complete lists from GEMA:
 
Caravan of Courage: An Ewok Adventure (1984) - Peter Bernstein
Morning of the Trek
Ewok Main Title
Good-bye Izrina
Gore-Axed Gorax
In the Gorax Chamber - Pt. 1
Rock
Bad Lands
Pixie
Wreckage
Prologue
Borra - Part 1
Borra - Part 2
Mace's Surprise
More Medicine
Chukha
Chukha's Song
End Credits (Feature Version)
End Credits (T.V. Version)
Ewok Party
Hungry
In the Gorax Chamber - Pt. 2
In the Gorax Chamber - Pt. 3
Kaink
Logray
Mace
Magic Pond
Medicine
Over There
The Planet #2
Serious Talk
Sick
Spiders
 
Known reel/part:
3m6.2 Wild Ride
10m1.3 The Cave
 
Ewoks: The Battle for Endor (1985) - Peter Bernstein
Alone
To the Cruiser
Escape
More Escape
Getting Out
Farewells
Cloak and Stagger
Caged
Dragon
Walking Talking
Remembering
Battle
Closer
Cold Steel and Hot Feet
End Credits (Feature Version)
Ewoks: The Battle for Endor - Closing Theme
Endor Jig
First Meeting
Interview
Justin
Main Title - Ewoks: The Battle for Endor
Marauders
Noa and Terak
Noa Whistles
Pie
Poker
Salak
Tssssh
The Wall
Wicket
Pursuit
My Star
House
Entry
Moving Out
Night Before
 
Known reel/part:
4m3 Noah's Ark
6m2.1-mg Interview

Here's a list from SABAM:
A SMALL DEMONSTRATION (2:15) - John Debney
ALONG THE WAY (02:38) -  Felton / Thomas / Vukcevic / Felton / Kilcoyne / Popson / Schmitz / Hetrick
ARABIAN BRIDE (00:08) - Damil Ahmed / Mladen Franko
BALTHAZAR ARRIVES (01:56) - John Debney
BALTHAZAR'S CAMP (01:45) - John Debney
BOO! (00:15) - John Debney
CASSANDRA RETURNS (00:20) - John Debney
CASSANDRA'S VISION (00:45) - John Debney
CHEER UP [Alt title: BEETHOVEN'S 3RD] (01:24) - Philip Alan Giffin / Eric Schmidt
DESERT FLOWER (00:30) - Elton Farokh Ahi
DIE WELL, ASSASSIN (02:55) - John Debney
ENEMY AT THE GATE (0:35) - John Debney
ESCAPE FROM ANTS (00:20) - John Debney
FAILED ATTEMPT (00:37) - John Debney
HAREM SCAREM (01:36) - John Debney
HEALING (00:50) - John Debney
I HAD A VISION (01:00) - John Debney
I STAND ALONE (03:45) - Salvatore P Erna
I'VE COME FOR THE WOMAN (03:30) - John Debney
IN THE CAVE (03:01) - John Debney
MARCHING IN (00:29) - Sho Kosugi
MATHAYUS ARISES (01:28) - John Debney
MATHAYUS MEETS MEMNON (02:38) - John Debney
NAYIBE (0:54) - Elton Farokh Ahi
NEFERTITI (00:48) - Elton Farokh Ahi / Farag
NEVER AN AKADIAN (00:55) - John Debney
NIGHT ATTACK (01:10) - John Debney
NILE'S BREEZE (00:09) - Elton Farokh Ahi / Sami-Choukri Farag
PICKPOCKETS (00:16) - John Debney
RETURN TO SENDER (02:29) - John Debney
SAHARA'S NIGHT (0:20) - Elton Farokh Ahi / Sami-Choukri Farag
SAVAGE WORLD (01:20) - John Debney
TEHERAN STREETS (00:42) - Roy Henley / Tro Khan
THE OASIS (00:37) - John Debney
THE SCORPION KING - MAIN TITLE (03:23) - John Debney
UNIVERSAL LOGO (00:21) - Goldsmith
VALLEY OF THE DEAD (02:08) - John Debney
VEILED THREAT (00:38) - John Debney
VISION OF DOOM (00:53) - John Debney
WILD RIDE (01:15) - John Debney
ZANUBA (00:40) - Gerhart Frei
 
A few more titles from SABAM:
AFTERMATH / OUTER SPACE
ALISA AND ROBOT IN BASEMENT
COUCH FIRE / ZORGONS FOLLOW
EJECTION / RESCUE
DUMBWAITER DOWN / BASEMENT
DANNY OPENS GAME
ZORGON SHIP UP CLOSE
 
Edit: here's some cues from the music sheets
2M9 v.4 Gravity/Aftermath
4M6/7 v.4 Shooting Stars/Run Upstairs
4M8 v.5 Astronaut Story
5M9 v.8 Basement/Getting Game
5M9 v.8 Pt. 2 (m. 108-206)
6M2 v.3 Zorgons On
6M6-7 v.3 Astronaut Talks To Brother/Morphing
6M8 (v.8) Explosion/Zorgon Invasion

Since we have a few "restored music" threads, I thought it would be an interesting idea to highlight some of the best worst micro-edited cues in films. Here are some that I've meticulously reconstructed so far:
 
Attack of the Clones
The Chase Through Coruscant
The Conveyor Belt
The Battle of Geonosis
 
Revenge of the Sith
Crash Landing
The Battle of Kashyyyk
March on the Jedi Temple

1m2 Main Title / 1m3 Stealing the Cross (Indy's Very First Adventure)

https://drive.google.com/open?id=1OjCjhwqMwuuyd4gKItk2IMC5bwleNgxy

It seems the early "it belongs in a museum" was inserted?

11m1/12m1 Overlap / 11m1/12m1 The Canyon of the Crescent Moon

https://drive.google.com/open?id=19N_B7mVeJ0rMyMiJ7vZv87Jsv7sGhbkl

It seems some of the music was replaced with tracked music when the explosion deleted scene was dropped

10m1 The Death of Kazim (Death of Kazim)

Here is the Death of Kazim in 4 videos:

1: As it appears on the Concord.

https://drive.google.com/open?id=13Q0NYmhXS-jj2ZtOrCq-Ee2f-yhcrud5

2: With all known to have been recorded inserts (10m1 Insert 1, 10m1 Insert 2, .

https://drive.google.com/open?id=1TrsZCG2TEJUl0dYkoJRlHVCCFS4IPeDO

3: With Insert A.

https://drive.google.com/open?id=1N2kPA5ycMVSr2AQSzXxw5eQ5wsGVAk7C

4: With Insert 3 (this is just a guess).

https://drive.google.com/open?id=1Zj8EOvwPQXSSTOL7bf_iY1_DYOrW4Euq

1m4/2m1 Escape from the Train (Indy's Very First Adventure)

https://drive.google.com/open?id=1eLmR09zDToqEpnFaNLsxSTZDflO4A1s0

This the original version of the music for the lion beat.

Indy arriving back at home seems to have been messed with:

I think originally the warm Indy theme statement covered the Mailbox reveal, In the final film it covers Indy entering the house and the shot of the dog. (The bootleg cues out there don't include the repeated bit of the young Indy motif used in the film, so I don't think it was microedited out of the CD, also when I played it through without editing footage, the grail theme didn't sync up to shot of the illuminated book.)

2m2 The Boat Scene

https://drive.google.com/open?id=15TcYpGE8oxJYYSAG8za-S92MomlQKrfF
 
In the final film you can actually spot a continuity error: right after Indy gets the Cross knocked away from him and it almost gets washed overboard, you can see that he still has the cross in his hands while fighting the goons.So it looks like that beat was added after scoring.

(The shot of Indy still having the cross after just having it knocked from his hands can be seen at 1:50 of this video: https://youtu.be/3XfWxeszXEI?t=110)

3m2a The Holy Grail

https://drive.google.com/open?id=15fGhUUZwcIon5xfA-jq1v8MGQFEjkyBi

The opening notes were edited out (you can hear Henry's theme when Donovan mentions him)

3m3 Father's Study

https://drive.google.com/open?id=1Oh6bBDA3aOvva067uVoiMK-QjuP_grpp

The opening was dialed out in the film, you can also hear Henry's theme in the beginning of the cue as Indy and Marcus arrive at Henry's door.

4m1 The Library (X Marks the Spot)

https://drive.google.com/open?id=1cQJ-VYMxeE16hz8bL7AOdozcERpsSl33

The music for the reveal of the Roman Numeral X in the middle of the floor was replaced with a toned down insert.

6m2 Discussing the Book

https://drive.google.com/open?id=11S6aZwvbFRwW2K4138Q8wi1sW4fxhQw1

This is the original ending without the Indy theme ending

6m3 Alternate Start / 6m3 Elsa's Betrayal

https://drive.google.com/open?id=1gAa170i9_YtRyjneBlZafjkBe08nG9AT

The unused ending for the reveal of Donovan is restored.

6m5 The Capture of Marcus (Marcus is Captured)

https://drive.google.com/open?id=12_rufb6allIbKHs5dthCXXCjF83wCgwo

The opening Nazi theme and spirited rendition of the Henry theme is restored.

7m2 Room in Flames (Alarm!)

https://drive.google.com/open?id=15emniE8-GzXYPYk4gjGyfkTZZ9jabg03

The original order of scenes has been restored as best I could figure.

7m4/8m1 To Berlin

https://drive.google.com/open?id=19QVLNG1Xpl0vTzKFd8U5gMNobYlPyKRd

The original ending is restored.

8m3 Meeting Hitler (To the Blimp)

Take 1: https://drive.google.com/open?id=1cgVGkqZ1afIl6Vh_mztgMqcGp8vxhKS3
Take 2: https://drive.google.com/open?id=1op9GbscDGaS1dYdpeEFCW0YB9wNa4sOM
Take 3: https://drive.google.com/open?id=1v2lmuAW0msaEFBi9lG6d0BO5N4uZfoNw

The music for Indy meeting Hitler has been restored, there were several sync options so I present three of the most likely.

8m7/9m1 Turning Around (The Blimp Turns Around)

https://drive.google.com/open?id=1E4SPUI1w_DS6kjRcHYv0zZ35qXaGacaH

The unused Grail theme statement in the opening of the cue has been restored.
 
The Biplane Chase (Keeping up with the Joneses😞

https://drive.google.com/open?id=146mI-RxV0QxgO0-PUCyky6Xtj6pkqxdK

This one was tough, though I think I might have figured it out mostly.

@Holko@Incanus@Jay@Datameister@Luke Skywalker@lairdo@fommes

Time for Last Crusade!

Here you go @Josh500. This is the score as edited in the film, to picture. 
 

 
Now, just because I enjoy this, here are the most noticeable differences (that are not super specific edits):
Right away, the opening is different, removing the Ticking clock and Chimes until around 0:11 2:09-2:38 retains the ticking clock in the film. This section has no ticking on the LLL set or the OST. 3:55-4:03 plays the Flutes a second time. It's not looped, but overlayed over the top of the cue the second time. 4:52-5:00 retains the ticking clock in the film. This section has no ticking on the LLL set. This section is also slowed down, you can hear the tempo change in the ticking. 5:17 onward the film does not feature ticking. This section is present on the LLL set and the OST. 8:49-End is slowed down quite a bit from what is on the LLL set. It plays at 117% it's original length.  
There are plenty of other edits, loops, tempo changes, etc. of course, but the above are the very clear differences. I also just want to say, this was a pain in the ass to replicate and it's still not quite perfect. Damn editors. Lol.

It seems the sequence underwent some editorial changes after Williams scored it. Some parts of the music run longer than the film (notably Sirius and Lupin chasing Pettigrew in rat form), while some parts of the final film run longer than the music. To conform the music to the scene I've removed some dialogue and created blank holes where the film has been cut down.

@Jay you might know from the sheet music, but what did the unused last 38 seconds of the Marauder's Map underscore?
 
I did a 'score restore' and my best guess is it belongs to this scene here, as Harry reads out the map's message to Snape (and ending as Lupin appears).
 

OK, added 2000s scores to the main post now!
 
 
2001 - Harry Potter and the Sorcerer's Stone
My Google Doc 2001 - A.I. Artificial Intelligence
My Google Doc Mike Matessino text interview by me on the 2015 La-La Land Records Expanded Edition, June 2015 2002 - Attack of the Clones
My Google Doc 2002 - Minority Report
My Google Doc 2002 - Harry Potter and the Chamber of Secrets
My Google Doc 2004 - The Terminal
My Google Doc 2005 - War of the Worlds
My Google Doc 2005 - Memoirs of a Geisha
My Google Doc 2008 - Indiana Jones and the Kingdom of the Crystal Skull
My Google Doc

I actually updated the sheets for 1 & 2 this weekend
 
Harry Potter 1
Harry Potter 2
 
I added tabs to HPCOS covering the recording session leak, and I put a new "Chronological Order" tab on both as well
 
Of course the LLL editions of each of these are only barely out of chronological order, and I don't personally feel the listening experience is improved by going into these tracks and editing them, but for those who want to, now you know how!

The problem with Williams OST"s is it takes  real fans  decades to get complete score. If he did like Howard Shore of Hans Zimmer and release a deluxe edition right away there would be no problem. Williams wants to please the general public but it never occurs to him he has  more hard core fans and never made an effort (until now because of MM) to please any of us.
 
It's having to wait for Oscar FYC's, looking in videogames and DVD menus that's the real problem with Williams OST"s

Here's a spreadsheet for HPCOS, it only has a tabs comparing LLL to OST for now
 
https://docs.google.com/spreadsheets/d/1Lenk84oELk7Uo6jN1ew4BTSDbfJvgJLfVxJxx2s_SKA/edit?usp=sharing

I've added tabs that include the session leak tracks in my HP1 spreadsheet
 
https://docs.google.com/spreadsheets/d/1B59r_jImSzoPfypk-qxe5bZMNjyKkZcpIcOAks4kzHw/edit?usp=sharing

Here's a simple spreadsheet for HP1 comparing the LLL album to the OST
 
https://docs.google.com/spreadsheets/d/1B59r_jImSzoPfypk-qxe5bZMNjyKkZcpIcOAks4kzHw/