The Ancient Brethren were mentioned in this Planewalker hook. That article is a glorious mess of references to all sorts of sources.
I believe there are hints of primal entities who speak the Language Primeval in Die, Vecna, Die!
The Language Primeval itself is mentioned in College of Wizardry, Die Vecna, Die!, and The Epic Level Handbook, and is closely associated with the True Words mentioned in Dead Gods and Vecna Reborn.
The Sleeping Ones, who exist frozen in the Paraelemental+Plane+of+Ice according to The Inner Planes, are also likely inspirations for the Ancient Brethren. The Sleeping Ones themselves are mysterious, vaguely Lovecraftian creatures.
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