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HoangNhatAnh said:
curl-6 said:

SNES: Mario Kart, Starfox, F-Zero, Pilot Wings

N64: Smash Bros, 1080 Snowboarding, Paper Mario, Animal Crossing, Sin & Punishment, Mario Party

Gamecube: Pikmin, Luigi's Mansion, Geist, Eternal Darkness

Wii: Xenoblade, The Last Story, Pandora's Tower, Wii Sports, Wii Fit

Wii U: Splatoon

Switch: ARMS, Labo, Ring Fit Adventure, Astral Chain

Also, some I'm not sure whether or not they're technically Nintendo IPs: The Last Story, Endless Ocean, and Pandora's Tower for Wii, Eternal Darkness for Gamecube. Can anyone shed some light here?

Nintendo owns all.

Jumpin said:

As a note, Wave Race 64 was a sequel.

And while Paper Mario became its own brand, the original game was developed and promoted as a sequel to Mario RPG.

I don’t think Geist and Eternal Darkness would count since these are third party games that were published by Nintendo, but were one-offs rather than franchises.

Nin owns Eternal Darkness trademark.

Pemalite said:

SNES. - Killer Instinct.
N64. - Perfect Dark.
Gamecube. - Luigi's Mansion.
Wii. - Xenoblade.
WiiU. - Nothing comes to mind.
Switch. - Astral Chain.

WiiU Splatoon.

mjk45 said:

Ganbarion developed the game Nintendo published the Pal version and Xseed published the NA version , so the developer most likely owns the IP.

Edit it turns out that Nintendo released a NA digital Edition later without Xseeds knowledge so they may own it , aren't you glad I cleared that up for you.

Nin owns Pandora's Tower IP.

According to the Nintendo online store the Pandora's Tower copyright is owned by both Ganbarion and Nintendo and The Last Story is owned by Mistwalker and Nntendo.
It seems to be the same situation that Nintendo has with Koei Tecmo, in which they both own half of the Fatal Frame franchise. Nintendo learned this approach from long time Nintendo partner Owe Bergsten who only ever buys 50% of a company so that they can be on equal terms rather than one ruling the other.
The rest is owned by Nintendo.