Layering armour was common, historically, for those who could afford it. Which lead me to the realization that I can't recall any rules prohibiting layering armour.
Although the d20 System is an exception-based rule-set, it still basis itself on "the common understanding" – That is, for example, real horses eat grass, so d20 System horses eat grass (unless a rule says otherwise), so Unicorns, which are based on horses, eat grass (unless a rule says otherwise).
From there, there is a train of logic: real armour can be layered, or designed to be layered; so d20 System armour can be layered, or designed to be layered – unless a rule says otherwise.
So: Can anyone quote rules either prohibiting or covering layering armour, or is there any RAW or FAQ covering it?
The rules do discuss layering armor—in that it’s already assumed that this is what you are doing and the benefit of doing so is already a part of the armor’s statted armor bonus to AC. For example,
That thick layer of padding is traditionally the same thing as padded armor. If you were to use leather or hide, instead, it would just be bulkier, heavier, and hotter—not any more protective. And it’s not mentioned here, but of course you’re wearing chain too, because that’s how full plate works: padding, then chain, and then plates over the top of that. The chain is mostly for joints where you can’t put plates, and is already factored into the +8 armor bonus to AC.
So long story short, you can’t get any benefit from layering multiple kinds of armors because the game already assumes you are doing that.
As a matter of rules, all armors provide an armor bonus to AC, and typed bonuses do not stack.
(emphasis mine, armor/shield bonus rules)
As for magic armors, there you are limited by the rules for magic item slots:
(rules for magic items on the body)
So if you wear two magic suits of armor, they don’t both work.
The Oriental Adventures exceptions
Oriental Adventures is a 3.0e campaign setting book for Rokugan (the same setting as Legend of the Five Rings), and it includes the wildly-ill-considered chahar-aina and dastana. These actually are modular armor layers that you can add to other items, giving them +1 more armor bonus to AC, at the cost of −1 more armor check penalty. They can only be layered with light armor, the chahar-aina effectively being a breastplate (and requiring medium armor proficiency) and the dastana being oversized bracers.
Both of these items represent an author basically misunderstanding how armor works. The chahar-aina should have just been a separate medium armor, noted as including layers of padding and/or chain, while the dastanas should have just been an unusual shield (3.0e didn’t have separate shield bonuses to AC, which may well explain the dastana by itself). They are frequently banned, even in games that are expansive enough to otherwise allow Oriental Adventures material. When allowed, they are “gimme” options that just about every character ever should use, which is why they usually get banned.