Interesting about the airship theme. Kondo based his new tune on the Mario 3 airship, but the Odyssey tune is definitely based on new version. Clever way of referencing the classic airship without going back to the obvious Mario 3 well again.

In Wii Sports Resort's Island Flyover Mode, if you go over to the light house you can hear Morse code which just translates to two people having a conversation about if people use Morse code anymore. Also in Splatoon 2 when you unlock new sub abilities on your clothes, you can hear a sped up version of the GameCube start up theme. This can also be heard in Mariokart 8 Deluxe when you get an item in Urchin Underpass.

Super Mario Odyssey's menus have several secrets like the ones in this video (pause + unpause = 1-UP jingle / pause + options + choose mode + cancel = Comet Observatory), but something often missed is the subtle noises made by the HD rumble as you scroll up and down; top-of-the-menu items have higher tones, and the further down you scroll, the lower the tone becomes. Try holding the controller near your ear while scrolling down a long list!
Similarly, a setpiece in the final level of Kirby Star Allies 'plays' the original Dream Land theme via HD rumble, but that's more of a "you 100%ed the game" obvious reward than a 'hidden' reference.

Adding to BOTW's morse code bit, I don't remember if it was canon or just a theory but someone said the morse code was coming from the champions before they died. And because they died, the sounds were left to repeat for 100 years until Link came to free their spirits. Mipha's is more frantic and appears almost instantly, as if she knew she couldn't fight on her own. Revali's appears late into the song and sounds terrified, as if Revali thought he could fight on his own, but only realized he couldn't when it was too late. As for Daruk and Urbosa's theirs is more calm and basic, as though they were simply accepting their fates (that doesn't sound scary).

Also, each time you activate the terminals inside the beasts, the morse code gets quieter before it disappears entirety.

I absolutely love that they included the Mario Maker airship theme into the beginning of Mario Odyssey. I remember first getting the switch and Mario Odyssey along with it, and hearing that was the coolest thing!!

First I find a channel I like, then I watch all of there content for multiple hours, and then I finish watching all of their content, left wanting more.
It’s a vicious cycle.

I don't know if this is common knowledge or not, but Mario Kart Wii's Bowser Castle's main melody is actually a slowed down version of Maple Treeway. In addition, most of Super Mario World's soundtrack is essentially the same leitmotif played in different ways - this carries over to the new arrangements in Mario Maker as well.

This one's not that obscure, but I don't know if i've ever seen anyone talk about it. The theme that plays when you meet the dragons in Skyward Sword is really similar to the Kakariko village theme in Breath of the Wild.

I forgot how good the Spirit Tracks overworld theme was... even if it was weird that you were playing it while talking about Breath of the Wild.

The Legend of Zelda: Spirit Tracks also has a neat little easter egg! The track "Byrne's Helping Hand" has Zelda's lullaby in it, which is quite interesting, as the entire OST is extremely sparse with direct references to older Zelda songs. Also very fitting, given when the song plays (which I shall not spoil).

The Gamecube part was the most interesting to me. It sounds so much different 19x slower. Really neat

The best part about the Famicom startup theme is that if we slow it down, we’ll get an 8 bit rendition of the GameCube home page theme.

Another really neat secret is that Sidon's and Mipha's names reference music notes, Sidon is Si + Do, which are B and C in a different notation used in countries like Italy or Spain, and Mipha is Mi + Fa, which are E and F. What's really neat is that in each character's theme, you can hear those notes back and forth in the main melody!

Those GameCube and Wii sounds around 7:40 sent chills down my spine. Thanks.

(2:20) Saying "translating morse code" is a bit weird, since morse code is just a different way of communicating letters. It isn't translated. That's like saying you translate text by changing the font.

I would love for this to become a series on this channel. Perhaps looking at other companies' game musics as well

1:28  iQue.  There you have it.  Nintendo's old Chinese brand name.

In the music for Rito Village from Breath of the Wild, it is quite easy to hear the Dragon Roost Island melody from The Wind Waker at a certain point.

You missed the big one
The main theme from Skyward Sword is the Ocarina theme from Ocarina of Time but backwards (I know the themes have names but I don’t know them because I’m not a Zelda fan)

Another interesting Easter egg of death mountain theme is in twilight princess water temple. The death mountain theme can sometimes be heard as part of a lower pitch background melody that plays underneath the mian melody.