Eternal Darkness. Once it started deleting all my data on the memory-card, i coudn't kill the enemy, i entered a room upside down and for some reason it managed to turn down the volume on my TV. That was a buggy mess

I've experienced a bug once in Super Mario World, but I can't remember much else.

Where are the bugs I read about, nut never encountered myself (therefore being of least bother to me):
Mario Kart 7 on 3DS had a glitch to that allowed to shortcut on one track, I read. There was a patch.
I also read, Pokemon X/Y had a gamebreaking bug in the capital city. I never encountered it myself and there was a patch.
I read too, that Super Smash Bros has a bug that potentially bricks the WiiU. I never encountered it, but I'm cautious about that one as you might understand.

There were some bugs I encountered myself. Obviously that bothered me more.
In Metroid Prime 3 on Wii I had a glitch on a boss (the one at the pirates, that flew around in an open space, I think that was the first one). He froze midair in a part of a sequence where I couldn't do him any damage. I tried, but essentially I had to reload and try again. Other than that Metroid Prime was flawless for me, so it was more an irritating thing at one time, nothing really bothering.

At launch of the WiiU many games had bugs at launch. That included Nintendoland. There was a day one patch for console and game, but as it was launch and everyone was downloading that, I postponed the patches to play first a bit. But one minigame in Nintendoland freezed on startup - every time (I think it was the Zelda-game). I gave in and downloaded all the patches first, playing first on the following day.

Luigis Mansion 2 on 3DS was a fun game, but multiplayer was ultimately glitched. I played some sessions and there happened nearly everything. This takes for me the crown as the most bug ridden Nintendo-games I played.

That said, I was shocked how glitched and bugged Ubisoft games were. Even Assassins Creed III, that I bought more a year after release and had big patches to download at first, had still ridiculous bugs:
https://miiverse.nintendo.net/posts/AYQHAAABAACNUKEdJanfoA
https://miiverse.nintendo.net/posts/AYQHAAABAAC_UqFKPY8NZw
Remember, this already had more than a year of patches.

That is what I heard from my neighbour... never played it -.-"

Ubisoft is like the kings of bugs, quite patetic at times.

And you made me remember the biggest bug over the internet... By mentioning Pokemon X/Y you made me remember Missigno that if captured would make your game freeze.

um maybe Mario Kart SNes.... Weird things would happen when I used the feather at certain times, other than that. Nope. 1st party Nintendo games are as clean as a virgin.

Grumble Volcano on Mario Kart Wii? I know is more an exploit than a bug per se, but it pretty much broke that track for online play, people couldn't help themselves.

Numerous Nintendo 64 games.

Super Mario 64
Donkey Kong 64
Ocarina of Time

Then there's Pokemon Red and Blue.

Hah, I got 999 coins in Delfino Plaza by collecting all the coins in the outer level, entering that minigame, beating it, and repeating the process until I got the max number of coins.

Good times.

I always thought the original Metroid was rather buggy. Tiles randomly flashing across the screen, scrolling bugs, sprites getting permanently frozen on screen, glitches with doors, etc. I'm not sure how much of this shows up in emulators, but on the real hardware the game felt unpolished.