His regular commentary to the Torah.
I.e. Mishneh Kessef Book II, also called Matzref L'Kessef.
His broader discussion of the book of Bereishis, Gevia Kessef.
Commentaries to Moreh Nevuchim.
The main issue is that some of the things he says are for lack of a better term "radical".
For example, in the post that you commented on, I was quoting him where he basically said that the view of Rambam (and some of Chazal) that Iyov didn't actually exist, essentially allows for the destruction of the whole Torah.
He says something similar in his commentary to Parshas Beha'aloscha, by the incident of Aharon and Miriam speaking ill of MOshe.
There he says it even more harshly, and accuses everyone (Rashi, Ibn Ezra, Onkoles) of using a methodology that destroys the whole Torah.
He took rationalism to an extreme, explaining some miracles in non-miraculous ways.
He is considered the prime proponent of the vieww that Rambam actually believed in (some form of) Aristotle's eternal universe.
(I mentioned that one in this answer:)
4
This was one of the hottest topics in medieval Jewish philosophy.
Saadia Gaon devoted the first treatise of Emunot V'Deiot to proving creatio ex nihilo and refuting the opposing arguments.
Here is an excerpt from his introduction to that treatise:
Therefore, O thou that seekest the truth, m...
He argues that Akeidas Yitzchak did not take place in reality.
He often interprets pesukim in ways that make it sound like there are many things that are not important, or exaggerations, or stylistic, or not conveying anything important.
Obviously, other commentators do this to an extent, but my impression is that he takes this further.
He often uses blunt language, especially when asserting that his predecessors were wrong.
He says that the books of the Torah that contain the mitzvos are less important (or less great, or something to that effect — I'll find the exact reference) than the books which contain the stories.
Similarly, he says that it's better to focus more on philosophy than halacha because halacha you can always just look up in the Mishneh Torah.
He says that Aristotle took a lot from the Torah.
He even says (somewhat in jest) that Aristotle knows the Torah better than us.
אוי לנו כי הם ידעו התורה שלנו יותר ממנו
R. Yosef Ibn Kaspi
R. Yosef Ibn Kaspi