→Horned monster that protects the humans.

It's also worth noting that Alphy's finds all her anime in the dump. Which means she watches literal garbage-tier anime.

Spoilers

I'm pretty sure the Pyrope enemy is a refrence to Terezi Pyrope.

This game has Earthbound written all over it

"Possible Inspirations and references in Undertake"

In the Omega Flowey battle, not only are there inspirations from Giygas, but Flowey's character is very similar to Porky's and it even boils down to extremely similar quotes used:

Mind if I contribute some more additions?

15:14

I think it's pretty well-known by now that Toby used the Final Fantasy VI, Earthbound and Chrono Trigger soundfonts in a few songs. "But The Earth Refused to Die"'s title is also a reference to the unique game over for Lavos in Chrono Trigger, "But... the future refused to change."

homestuck/undertale land similarities:

You missed the touhou references. The structure of Undertale's story: A bunch of monsters get driven underground, is very similar to the backstory of touhou 11 where a bunch of oni and youkai were driven underground. Flowey's bullet patterns are also really similar to the bossfight Marisa Kirisame. There are others but I don't want to go on forever x3

Ness calls Dad:

Here's a little contribution as well, this game uses TONS of Chrono Trigger's sound samples from it's soundtrack, mostly in the tracks ''Battle against a true hero'' and ''Reunited'' in Chrono Trigger, the whole game revolves around time travel, something that sans is known for doing and knowing a lot about, a fun fact is that in Chrono Trigger's soundtrack, there's a piece called ''Determination'' which is used in moments where the characters don't give up to give peace to earth.

Anyone else thought of Yukari's(touhou) hat when seeing the hat of Tsunderplane?

Death by Glamour is based of one of Toby's own creations, Noisemaster's Theme from Cucumber Quest. It also along with Core, Another Medium and Waterfall is based of an unfinished Homestuck song by Toby called Patient, which was meant to be a counterpart to and remix of Doctor(a Homestuck song by George Bunzinkai, Micheal Vallejo and Clark Powell) . Doctor is also inspired by Moonsong from Cavestory (I don't know the artist).

Amalgamate is probably also inspired after the battle with the Circus Tent in Earthbound as well, since that is the only other battle that really takes up the screen in that game.

The ruins looks reminiscent of Derse

Looking into Homestuck would be very relevant. Homestuck, like Undertale, happens in a world inside a game, where the game mechanics become relevant plot elements.