I gotta check a few of these to be sure, but pretty confident these delistings are/were correct:
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Amazing Spider-Man 1 (Ultimate edition) -
Activision lost the rights, physical copies still around.
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Amazing Spider-Man 2 -
Activision lost the rights, physical copies still around
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The Cave -
Publishing rights reverted back from SEGA to Double Fine, who would need to publish the game themselves if they wanted it back on Wii U. PS3, Xbox 360 versions are also delisted, still available on Steam though.
-
Donkey Kong Country: Tropical Freeze - Was temporarily
delisted in NA region, conveniently around the time of the Switch port. Apparantly an error,
should be back up, but I haven't checked.
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Earthlock: Festival of Magic - Recently delisted when Earthlock got a major upgrade on almost all platforms except for Wii U. I remember reading on MiiVerse the Wii U version suffered from frequent crashes, perhaps they were unable to fix them?
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Mario & Sonic at the Socchi 2014 Olympic Winter Games - Likely lost the Olympic license, physical copies still around.
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Mario & Sonic at the Rio 2016 Olympic Winter Games -
Delisted in December 2017. Likely lost the Olympic license, physical copies still around.
-
Meme Run - Delisted following a
DMCA claim by the owner of the trollface meme.
-
Mighty No. 9 -
Delisted from the JP eShop June 2018. Not sure if this is worldwide. Physical copies exist.
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New Super Mario Bros. U - Now only available as download in combo pack with New Super Luigi U
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One Piece World Unlimited Red -
Delisted in July 2017, physical copies exist only in PAL/JP regions.
Then there's a slew of licensed games all of which I would need to check, but I'm imagining some of the following will definitely disappear at some point, if they haven't already:
Adventure Time (2 games), Ben 10 Omniverse (2 games), the Cartoon Network fighting game, How To Train Your Dragon, Turbo that racing snail, The Smurfs 2, Transformers (2 games), Penguins of Madagascar, Rise of the Guardians, I think there was a Barbie game too.
Hello Kitty Cruisers is definitely still up, went on sale recently. I'm not sure how the Disney products are faring, there's Planes: Fire & Rescue, and the late 2017 release of Cars 3, might be more. There's also a bunch of LEGO games of course, and the Just Dance titles must be a licensing nightmare as well...
EDIT: There's also some video services in various states of delisting. HULU is definitely not up in Canada, might be delisted in USA too. Don't think it was ever in many of the PAL areas. Netflix's app reportedly had a disastrous update recently which crashes the console if you don't exit out to the Home menu during the credits before finishing a movie/episode entirely. Might be delisted in some PAL areas already. Think I read that somewhere, could be wrong. Not sure about Crunchyroll.