They don't, except for when they do

Edit:
So I want to clarify what I said about Bach not writing the Toccata and Fugue in d minor.
There's been a lot of discussion on the subject, and from everything I've gathered the answer is that this piece is one of the more anomalous in Bach's repertoire which, along with the lack of an original score written in Bach's hand, makes his authorship of the piece seem somewhat less that certain by a handful of Bach scholars.
However, until there is more substantive evidence, the convention is to attribute this piece to Bach.
So "Bach didn't write the toccata and fugue in d minor" may have been a little too strong here, maybe even misleading, and I just wanted to take a minute to completely clarify that point.
The quote from Jean-Claude Zehnder is "The matter still remains open, despite the scholarly discourse that began in 1981. Until proof of the contrary, BWV 565 should be considered as a work by Johann Sebastian Bach."

oops.

https://en.wikipedia.org/wiki/Toccata...


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Sources:

A fantastic source on trying to decipher how much Bach actually appeared in the silent film cannon, as well as some scoring conventions of the time:
Status, Standards, and Stereotypes: J.S. Bach's Presence in the Silent Era
James M. Doering
https://search.proquest.com/docview/2...

A brilliant article about the 1931 Dr Jekyll and Mr. Hide, I doubt I would've ever noticed that the organ in the opening was transposed down a minor third and this article shed a lot of light on one of the first ever horror soundtracks:
The Strange Case of Rouben Mamoulian's Sound of Stew: The Uncanny Soundtrack in Dr. Jekyll and Mr. Hyde (1931)
http://www.columbia.edu/itc/film/gain...

Basically everything you could ever want to know about the narrative themes and significance of organs in films.
I cannot stress enough how valuable this source was and if you're at all interested in what a musical instrument could represent then you owe it to yourself to give this a read:
Carnival of Souls and the Organs of Horror
https://www.academia.edu/3138033/Carn...



There are also a LOT of articles that outline the history of the Toccata and Fugue in d minor and its presence in film history, there's just too much to organize and they overlap a lot so I'm just going to link them all en masse here:

https://www.wqxr.org/story/what-makes...

https://www.cbc.ca/news/canada/britis...

https://www.cbc.ca/news/canada/britis...

https://blog.oup.com/2012/08/pipe-org...

https://theconversation.com/the-pipe-...

https://www.wqxr.org/story/what-makes...

https://books.google.com/books?id=iGN...

https://www.classicfm.com/music-news/...