i mean nintendo first party games.
I will expand first party to include things they publish and/or own the rights to -- nobody would say Pokemon is not Nintendo's baby despite various business quirks so going with similar logic there. Might mention a few Satellaview games here (even if most of those are fairly small, remakes or cut down, the big ones like the Zelda have been mentioned already but you might still want to explore it) but will largely skip things like the pikmin ereader and other such things.
The Band of Thieves & 1000 Pokémon could be worth mentioning here -- was kind of a streetpass (so 3ds) pokemon battler a few years before pokemon go.
I am not sure where to classify Itadaki Street for the DS -- it features Mario on the cover (along with a slime from Dragon Quest) but was Square Enix handling publishing duties. Think Mario Party but maybe with a bit more board game element.
I will similarly skip the earlier Nintendo arcade efforts -- Space Fever and SF-HiSplitter being Nintendo's take (or shameless clone as the case may be) on Space Invaders.
By similar token there is a Mario Party arcade game made by Capcom.
As mentioned above they often contribute their main characters to various mahjong (as in the multiplayer game popular among older Japanese people, not the solitaire that forms the basis of essentially every Western game called mahjong), picross and other puzzle games.
Do we have to count the Japanese dictionaries for the DS? There was also a Japanese writing/language trainer game or two.
Equally sometimes Europe will get a title that elsewhere might not, and several times North America got things that most in Europe would likely have known nothing about before the internet. Not a Nintendo game but Bomberman 2 is worth a look if you can get past gangly bomberman (still have to sort that as a hack) and only appeared in Europe and Japan. Depending upon the timeframe then Europe has also occasionally had games before North America -- usually if they can't make enough for the Christmas rush or something, however as we are talking about released games then you can go read up on that for yourself (though I will note your beloved Zelda Minish Cap hit Europe a few days after Japan in November 2004 but the Americans had to wait until January the next year, the salt did flow on this site as well).
Starfy, a really nice platformer series, is owned by them and had one DS entry appear outside Japan. The lack of this one boggles my mind and is one of the few Nintendo properties (advance wars being the main other) I actually care about.
For the DS then ASH Archaic Sealed Heat. There is a translation but it was a leaked version so play it as you will.
Sticking with RPGs Nintendo had a hand in on the DS and never brought out of Japan. Soma Bringer,
https://gbatemp.net/threads/soma-bringer-open-translation.78947/ for a translation.
Kousoku Card Battle: Card Hero. Card Hero has yet to make it out of Japan. Same people as do Fire Emblem and Advance Wars (don't know what team within though) but being a card game (if it is not YuGiOh or Pokemon, maybe occasionally Magic the Gathering, nobody really seems to care about such things outside Japan, which is a pity as the former two are seldom great games)
Rhythm Tengoku. Music/rhythm game, not bad either.
Animal Crossing is known as Animal Forest in Japan and has a few exclusives.
If you like Animal Crossing then also look up GiFTPiA, I dare say there is a reason it did not make it outside where something like Rune Factory might have but very much a suitable entry for this list.
Mentioned Mother 3 already but here because it is notable. Mother 1 also counts in this (2 appearing as Earthbound in North America at least).
Doki Doki Panic. This was Super Mario Bros 2 outside Japan as Nintendo basically tweaked the images to be Nintendo characters and shipped it, why it is also quite the departure from other games. However basically everybody know this at this point in time.
Ginga no Sannin. Technically a Nintendo funded port of an Enix RPG called The Earth Fighter Rayieza.
Yūyūki. FDS (famicom disk system, NES/famicom addon for those unaware. One of the various takes on the monkey king story.
Snoopy Concert (yes as in the cartoon with the white dog with black ears and small yellow bird), technically developed partially by Nintendo but published by others.
Kururin. One of the GBA titles appeared in Europe but there are plenty of other games got back before and since in the Kururin
Excitebike had a Nintendo character themed Satellaview title.
Magical Vacation, did see a sequel make it out of Japan for the DS by the name of magical starsign (was one of the three games released over a day or so that broke the DS RPG drought early in its life)
Joy Mecha Fight. NES/famicom exclusive, made by Nintendo and considered a somewhat notable early fighting game in its own right (not the first, but surprisingly good for the time)
DS Uranai Seikatsu, a fortune telling game for the DS.
Shin Onigashima. NES/famicom, one of a series of games being Japanese folklore but text adventure.
Kiki Trick. One of the many minigame collection/party game collections for the Wii, however one Nintendo's in house devs made and they published.
Fatal Frame 4/Fatal Frame: Mask of the Lunar Eclipse never made it outside Japan (was planned, later cancelled) and Nintendo published it.
Mario & Wario. SNES game using a mouse seeing you guide characters around, think kind of prototype Mario vs Donkey Kong.
Slide Adventure MAGKID. One of the DS slider games.
bit Generations. Surprisingly tight minigame collections (they were quite popular when they dropped around here), Japan only for the GBA.
Though if I am mentioning this I guess I will mention Nintendo game seminar that saw a bunch of experimental and small games drop for various downloadable game services
https://nintendo.fandom.com/wiki/Nintendo_Game_Seminar
Koro Koro Puzzle Happy Panechu! A tilt sensor game on the GBA.
Tingle's Balloon Fight DS and a whole bunch of other Tingle games. Remember the green suited annoying character from Wind Waker? Has a whole spinoff series (the one named back there even being a Nintendo Club exclusive rather than retail), one appeared in Europe, one got translated
http://www.romhacking.net/translations/3376/ and the others are doing whatever.
Various Fire Emblem titles appear on far older consoles than remakes that might have made it out of Japan, or indeed have yet to make it out of Japan. Mentioned some already.
Custom Robo has many more titles than the two that have made it outside Japan (North America got one a while back, and there is a worldwide DS version).
Tomodachi Collection. A mii based game for the DS, one of the few.
Tomato Adventure, from the people that would eventually bring you Mario & Luigi: Superstar Saga and in much the same line of thought. Partial translation
https://legendsoflocalization.com/tomato-adventure/ , various efforts to continue it with some talented people are out there but no real links.
Other than my dalliance with bomberman then that should be most of the notable, and less notable, games stuck in Japan that Nintendo and/or devs they outright own had a major hand in. There are likely a whole bunch of "yeah you can use some artwork" puzzle games not mentioned here, however I don't think any the ones I have seen would be my first choice for thing to translate but we might get another Dexter's Lab chess situation (by far and away my favourite GBA chess game even with the Dexter's lab skin).
