Willy Wonka & The Chocolate Factory is missing the bonus features on the DVD disc exclusive to the 40th Anniversary Ultimate Collector's Edition.

Casablanca is missing the bonus features on the second BD exclusive to the 70th Anniversary Limited Edition Giftset (almost 7 hours of documentary features!).

The Lord of the Rings and the Hobbit 4K trilogy sets have no bonus material. Even the Middle Earth collection, which has movie BDs with some bonus material, does not include bonus discs that came with the Theatrical versions, and none of the many Appendices bonus discs that came with the Extended versions.

It's a Wonderful Life does not include two features that were on the BD release: "The Making of It's a Wonderful Life" featurette and Theatrical Trailer

The Ran 4K release from Lionsgate does not include any of the extras from the previous Blu-ray edition. Nor does it include the bonus features disc that Studio Canal created for Ran 4K releases in all other countries, which included all those old extras plus newly created ones.

Star Trek: The Original Motion Picture 6-Movie Collection does not include the "Captain's Summit" bonus disc/feature that accompanied the Star Trek Original Motion Picture Collection from 2009.

Raging Bull is missing a number of features from the 30th anniv. Blu-ray: "The Bronx Bull" and "Raging Bull: Reflections on a Classic" featurettes, "De Niro vs. La Motta: Shot for Shot" comparison, 1981 Cathy Moriarty Tonight Show interview, and the LaMotta Defends Title newsreel footage

Spaceballs is missing the photo gallery "The Costume Gallery", and additional commentary tracks in Mawgese and Dinkese. It's also missing a vintage "Spaceballs: Behind the Scenes" featurette and a different theatrical trailer, which were on the original DVD release, but that DVD was included with some of the Blu-ray editions.

Robocop omits a number of production featurettes: "Flesh and Steel: The Making of RoboCop", "1987 Featurette: Shooting RoboCop", and "1987 Featurette: Making RoboCop"

Reservoir Dogs is missing the commentary from the DVD/BR releases.

Aladdin
4K Signature Collection does not contain a large number of extras on-disc that were included on the Diamond Edition Blu-ray.

The Little Mermaid
4K Signature Collection does not contain a large number of extras on-disc that were included on the Diamond Edition Blu-ray.

Beauty and the Beast
4K Signature Collection does not contain a large number of extras on-disc that were included on the Diamond Edition Blu-ray and Platinum Edition DVD.

The Lion King
4K Signature Collection does not contain a large number of extras on-disc that were included on the Diamond Edition Blu-ray and Platinum Edition DVD.

Scrooged
Missing the theatrical trailer

The Princess Bride
Criterion 4K is missing the following supplements from the MGM 25th Anniv. BD: 2 audio commentaries, Part 2 of the "True Love" featurette, "The Dread Pirate Roberts: Greatest Pirate of the Seven Seas" featurette, "Love Is Like a Storybook" featurette.

Ronin
Missing the "You Talkin' to Me?" featurette from the Arrow BD, though it's unrelated to the movie

Paths of Glory
Does not have any of the extras from the Criterion BD

The Killing
Does not have any of the extras from the Criterion BD

Killer's Kiss
Does not have any of the extras from the Criterion BD

The commentary wasn't actually on the BD (in the US anyway). The 4K is missing a pop-up trivia track though from the original BD, but more troubling is the hours of extras from the DVD versions that have never been on the BD or 4K versions.

Pan's Labyrinth
Missing the following features from the Criterion BD: Interview with Del Toro and Funke, Interview with Doug Jones, Ivana Baquero Audition

Cinderella (1950)
These extras from the Diamond Edition were not included: Deleted Scenes, Unused Songs, "Tangled Ever After" short

Punch-Drunk Love
Missing the Jeremy Blake interview, Cannes Film Festival, and The Pudding Guy featurettes from the Criterion BD. Edit: All included on the Criterion 4K that is now out.

Snow White
Missing from 85th Anniv. Edition: "10 Ways Snow White Changed Animation Forever" featurette. Missing from Diamond Edition: "Some Day My Prince Will Come" music video, "Disney Through the Decades" featurette, "Hyperion Studios" full feature

Aliens
Missing "Aliens: Ride at the Speed of Fright" and a TV spot from the Alien Anthology box set.

Who Framed Roger Rabbit
Missing "Toontown Confidential" trivia track

The Nightmare Before Christmas
Missing Vincent short film, The Worlds of Tim Burton's The Nightmare Before Christmas, Deleted Scene: Jack's Scientific Experiments, and the "On Track" version of What's This? Jack's Haunted Mansion Holiday Tour

The Departed
Missing theatrical trailer

Ip Man
Missing Disc 2 (bonus features)

I can’t believe I’d never heard about this site:
DVD Double Dip- Home

For extras collectors, it does a great job of showing you what extra features are available on what editions of DVD, Blu-ray, and 4K.

It’s not entirely comprehensive (mostly only mainstream titles, and even some popular ones (like Wizard of Oz) are inexplicably missing). Also, while it’s still updated regularly, some newer reissues, especially new Blu or 4K editions, are missing from the comparisons. Nevertheless, I think it’s the most comprehensive site of this type.

I often use https://www.dvdcompare.net/

That's all right, but you have to filter out the other region releases, and you can't compare directly across format releases (DVD vs Blu-ray vs 4K features). And comparing the features in a linear listing is harder than the matrix listings on dvddoubledip.com

Fargo
Trivia Track missing

Paranorman
Preliminary Animatic Sequences missing

Transformers: The Movie
"The Cast and Characters", "Rolling Out the New Cover", "Transformers: The Restoration" featurettes, Animated Storyboards.

Trainspotting
Missing Cannes interviews, The Making of Trainspotting, Trainspotting Retrospective

Casino Royale
Missing the following features: Director and Producer Picture-in-Picture Video Commentary, Bond Girls Are Forever, The Art of the Freerun, Catching a Plane: From Storyboard to Screen, Storyboard Sequence: Freerun Chase, Filmmaker Profiles

Enter the Dragon
Missing all of the special features (except audio commentary) from the previous Blu-ray releases (Criterion, 40th Anniv., and regular)

Mallrats
Does not include the TV version or Intro to TV version from the Arrow Blu-ray release. Does not include "View Askew's Look Back at Mallrats", "Mallrats: The Reunion", 6 easter eggs from the Universal Blu-ray.

North by Northwest
Missing "Cary Grant: A Class Apart", trailers, isolated music score, and Still Gallery.

The Fugitive
Missing pilot episode of 2000 Fugitive TV series

Titanic
Missing "Titanic: The Final Word" documentary, half of the Behind the Scenes feature, construction time lapse, skits, TV spots, and trailers

Once Upon a Time in the West
Missing theatrical version

No Country for Old Men
Missing "Press Timeline" features from Special Edition Blu-ray

Eyes Wide Shut
Missing "The Last Movie: Stanley Kubrick and Eyes Wide Shut", Interviews

Scrooged
Missing trailer

Amadeus
Missing Director's Cut, Audio Commentary, and Trailer