1. Mario Kart: Double Dash. Still my favorite Mario Kart, especially the absolute chaos on Baby Park...
2. Fire Emblem: Path of Radiance. Not quite as good as it's successor due to more standard story, but still one of the best Fire Emblem games.
3. Paper Mario: The Thousand Year Door. Even better than the first one.
4. Gladius. Tactical battles in a fantasy counterpart of the Roman empire? Count me in!
5. Chibi Robo. So much fun to play and exploring the house when you're just a couple inches high.

Yeah this would be my #2 behind RE4, absolutely phenomenal game, from its stunning visuals to its insane sense of speed. Hard as diamond nails, but great.

Prince of Persia: The Sands of Time

Cubivore: Survival of the Fittest.

One of the lowest print runs of any Cube game, if not the lowest. 

Eternal Darkness: Sanity's Requiem.

And the story mode was actually really good that you don't often see in arcade racers.

Oh yeah, that game! XD. Was an original game for the 64DD. As many of those, had to be ported to a N64 cart, and was finally cancelled (like many others) but had the luck to be ported to Gamecube. The N64 version was leaked some years ago, and apparently is complete.

Only US saw it in western countries. In Europe, Nintendo had the balls to launch the Gamecube version of Doshin the Giant, another game from the 64DD which in this case was also released in 64DD (one of its few games). The Gamecube version was translated (and dubbed!) to a bunch of european languages, all of them in the same disc. It is a very strange but nice game.

I'd honestly like a port or remake of that game to try it out. It got rave reviews back in the day.

Maybe Switch 2 will be like GameCube and have it least two M-rated Nintendo games.

GameCube had Eternal Darkness and Geist, Switch has Emio.

Bayonetta 2, 3, and Conker don't really count. They were published by Nintendo, but Nintendo doesn't own the IPs. But I guess in all fairness Eternal Darkness and Geist weren't developed in-house.

Luigi’s Mansion.