Asklemmy

Legend of the Mystical Ninja has a Gradius style video game inside of it that was so good that when I quit playing it I had completely forgot I was inside another video game.

Mario Party 5 has a side game (not a mini game) called Card Party that is good enough to be its own mobile game.

Any love for DOOM 3’s Super Turbo Turkey Puncher 3? It was so dumb but I will admit to loving the way you interact with computers and terminals in DOOM 3

Probably not what you are asking for, but the character creation process in the Traveller ttRPG is a great mini game. You basically take a person from 18 to however old you want, and their life path is dictated by your choices and random dice outcomes. It's a lot of fun. You can end up with a retired admiral, a prisoner or criminal, psionic, etc. Going through this process with a table of friends let's you build in rich fun connections along the way. The actual RPG then starts with mature, connected characters with a history, instead of 4 randos meeting in a tavern. In the classic Traveller you can even die in character creation. Current iterations removed the death component but you can be maimed from accidents in your career and start the game with a mountain of medical debt.

Ratchet and Clank: Up Your Arsenal had a side scrolling Captain Quark game that was quite good

Pretty much every minigame in Majora's Mask is making you forget the world is ending

I hate minigames, the only one i tolerated was Gwent in Witcher 3.

Didn’t rocket league originate from a minigame ?

The hunting game in Oregon Trail.

I thought of another one. There is a minigame in Xenoblade Chronicles 2 called Tiger! Tiger that is great. it is basically an arcade game where getting certain scores gives you credits that can be redeemed for upgrades for some characters. The minigame is randomized and has three different difficulty tiers and is overall really well done.

Not sure if it will count, but the Ancient Cave in Lufia 2 (SNES) was a game in and of itself. It was basically a roguelike dungeon. 100 random floors, it reverts you to level 1 and there were rare special items you could sometimes find in runs that could be brought back in. Beating the Ancient Cave is much, much harder and more rewarding than beating the game itself (storyline aside).

Treedude in superhot

And... Umm

Mario party

I loved the Showtime crashes in Burnout Paradise. I know most people would say that it was a sorry excuse for a replacement to the Crash mode that came before in the previous Burnout games, but I never played any other than Paradise so I can’t compare

the game.

Don't know if it would count since it's used in a couple levels, I think, but PVZ Reflourished, Caliginous Carnival. The levels where you essentially have to pay attention to the zombies beneath the hats and guess which is the weaker one in order to make the spawns easier to deal with. Rinse and repeat multiple rounds until you win. Would absolutely love to see that done more.

Also, along the lines of PVZ, iZombie is definitely up there for my favorite minigame in the series and in general. It absolutely sucks both versions of PVZ2 killed it (unless I'm wrong and the Chinese version still has the old PVP mode, but even then wasn't nearly as fun as the original minigame, nor anywhere near as balanced when half the time you'd find other players had level 4/5 plants that instantly destroy everything in 0.001 nanoseconds).