By the rules, would a gnome get a penalty on intimidating a human because they are small?
[RPG] Do you get a penalty to Intimidation checks if you’re a smaller size
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No, you don't. The section on Intimidation in the PHB says nothing about there being bonuses or penalties based on relative size. It's entirely dependent on your Charisma score, Proficiency bonus and whatever additional features you've picked up to boost your intimidation skills.
Of course, the DM still has the freedom to apply Disadvantage when it makes sense, but size alone probably shouldn't be the deciding factor there. It might make sense for a Gnome to have Disadvantage when trying to intimidate an Orc into laying down his arms in a face-to-face confrontation when both sides have weapons drawn and ready, but there's no reason to believe a Gnome is less intimidating than a Human when the same Orc is a tied up prisoner and someone is threatening to cut their tongue out.