hold up i've got a bunch of these
The Cluster/Gem Drill from Steven Universe. It's meant to sound like the Cluster is screaming in pain and it sure does it well
Plasm Wriath and
Mysterious Life Form from Pikmin 3. Plasm Wraith is the fight music and Life Form is the chase music, but both are pretty creepy sounding. (Mysterious Life Form is creepier in my opinion though.)
Giygas' Intimidation from Earthbound. It's just static with a slight rhythm. Bonus points because Giygas looks like this
The Void from Amazing World of Gumball. Its more surreal sounding than creepy, but the Void itself is creepy enough
For the final level of the game, the
Wistful Wild theme from Pikmin 2 is... ergh. The song is very nice, but the underlying minor piano and the bit at about 1:40 is... something...It just feels like something is wrong.
The Final Trial from the first Pikmin is also 'upbeat but something is off'. Actually, the Pikmin games in general have some odd music. Probably because they hide the dark stuff (in 1, Olimar is going to die, in 3 Koppai is going to starve, 2 has the President being held hostage if you take too long, although there isn't a time limit,) under cute creatures and bright colours. If you want to go through the whole soundtrack, you'll probably find some creepy gems.
(Warning! I found loads of creepy Zelda songs! Lots!)
Shadow Temple from Ocarina of Time. I heard someone call this temple 'The Paris Catacombs' once.
Stone Tower Temple from Majora's Mask, both
Normal and
Inverted
The original
Fire Temple music from Ocarina of Time. It's only in 1.1 versions of the game. The ominous sounding Islamic (I think) prayers in the background is what really makes it unnerving. Although as someone who owns the 3ds version, the original isn't all that normal sounding either, even without the chanting.
Forest Temple, also from OoT. It makes me feel lost, even with the hopeful flute. All of the Temple themes are great actually.
Ganon's Tower, another OoT song. Ganondorf's got some sick organ skills.
Earth Temple from Wind Waker. Besides my own procrastination, this temple is what slowed me beating the games. This song, the tomb-like aesthetic, and Re-Deads freaked me out, man.
Wind Temple, the second WW temple, sounds much more child-like (and since the koroks are evolved Kokiri, it makes sense) but those continuous violins (?) in the back are odd.
Ikana Valley from MM. Its the go-to creepy song for some youtubers.
Clock Town (Third Day) also from Majora's Mask. It takes the normally happy Clock Town theme, speeds it up, and puts an underlying sense of unease under it. Probably because everyone's about to die
Happy Mask Salesman's Theme, also a MM song. It's a remix of the Song of Healing, so it shouldn't be creepy, but combine it with this face and...
(There was a
super cool Majora's Mask fanimation awhile ago,
Terrible Fate, it gets the tone of the game down pretty good.)
Your Best Nightmare from Undertale. Let's just say the title is right.
Gaster's Theme, also called Dark, Darker, Yet Darker, is repetitive (Is it not done yet or something? I mean since Gaster doesn't really seem to properly exist) and creepy.
golly I hope this was helpful