Or maybe not. You decide.
Pseudoscience in music theory is a description of a structure where there's no inherent structure. An attempt to catch patterns in a noise, patterns which are one-off and don't help in composition. Patterns which don't exist in minds of listeners until they become deeply immersed in your theory.
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Jonathan Christian Petty. Wagner's Lexical Tonality. An author claims that keys in Wagner operas bear a wordable meaning, and every key change means a new meaning. For some reason, this work doesn't seem to be referenced in any other research and is largely ignored by a scientific community. The author explicitly mentions that his research is falsifiable.
Also see this
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David Huron. What is a Musical Feature? Forte’s Analysis of Brahms’s Opus 51, No. 1, Revisited - An example of a statistical disproof of someone's theoretical claim
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Explanations of why we build chords the way we build them. Eg. undertone series
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Affect theory
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Guerino Mazzola. The Topos of Music
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Adam Neely. A = 432Hz (Adam is great, 432 Hz is weird)
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The Lydian Theory by Brett Clement - I've just found this discussion, I don't have my own opinion yet
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Studies that claim that different keys employ different features in composers - I'm not sure that's 100% true. See Steven Bradley Yan. Aspects of Mozart's Music in G Minor and think for yourself
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A review of Matt Levine's formulation of a chord/scale theory
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Michael Buchler. Are There Any Bad (or Good) Transformational Analyses? - A case against transformational analyses and methods without preference rules.
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Ethan Haimo. Atonality, Analysis, and the Intentional Fallacy, review
It's great that theorists seek more tools to capture and describe the structure of music. It's like mathematicians trying to help physisists. Still, we should keep in mind that ultimately not all of the models will be useful or fruitful. While neo-Riemannian theory is pretty developed, for me it's currently on the edge of that. There's a lot of tools developed. Have we derived breakthrough understanding through it?
See the discussion on neo-Riemannian theory in Daniel Shanahan. Empirical Musicology: An Interview with David Huron, Part II
Same as a previous paragraph. A search for better models is great, but we need to question whether we got something from them so far.