So I am world building settings which do not arbitrarily delineate between "magic" and "nature". Here magic is the applied knowledge of manipulating the universe, analogous to technology. Rather than any kind of "magical background field", if necessary to explain, magic draws its power from somewhere specific like the movement of tectonic plates, the flow of ley lines, the pull of celestial bodies, etc.

This means that concepts like "magic damage" as in typical D&D don't make sense. Demons and werewolves and such aren't resistant or immune to "non-magic" damage, because "non-magic" doesn't apply to anything. Likewise, they don't deal "magic" damage because magic is a field of study, not a type of energy.

What exactly do I replace that with? What is the in-universe logic? There's a lot of leeway here.

P.S. Part of my inspiration for this comes from a blog post questioning the logic of damage reduction in 3.x: https://alzrius.wordpress.com/2010/12/13/647/

Another is Sean K. Reynolds' old "Curse of the Moon" book, which replaced the werewolf's resistance to non-silver with a block of bonus hit points that applied to all incoming damage (including magical) except silver. I haven't read it in a while, but IIRC the rationale was to make the silver weakness more important rather than allow it to be ignored by all other damage types like acid, cold, fire, magic missile, etc.

Another is the TV show "From Dusk Till Dawn", which had demons that were immune to earthly weapons but not xibalban blades (i.e. blades forged in the mayan underworld). This had some pretty interesting implications IMO, as it meant the demons were only invulnerable on Earth where demon blades weren't common.

I guess the sort of atmosphere I am going for is one where the heroes have to get the weapon they need from a particular smith, rather than having any old mage place a miscellaneous enchantment that works against anything. I just doesn't feel like the myths and fairytales that inspired fantasy, IMO.

It sounds like the magical energy or material you need to whack something with just becomes the same thing with the magic tag dropped off.

It is just fire instead of magical fire, silver weapons made a certain mundane, but specific way instead of magical silver, etc.

You'd only want spell resistance for things that directly screw up actual spell casting /energy gathering.  This might still be demons and such if an otherworldly presence interferes with the worldly process of magic.

Doesn't this literally date back to Beowulf?  Beowulf's sword couldn't hurt Grendel's mother, but there happened to be a magic sword in her treasure hoard that did the trick (though it then failed its saving throw and dissolved).

In LFG I went with silver weapon vs lycanthropes & aberrant terrors, and cold iron weapons vs demons & undead. So those special metals bypass or suspend the target's usual regeneration or immunity or whatever. Such wepaons are rare/fiddly/expensive to make, but not as rare as an enchanted weapon. Also holy water burns undead/demons.

One of the big differences between mythology and the magic weapon mechanic is that mythological weapons are typically unique, whereas there are innumerable "magic weapons" (same for silver weapons, iron weapons). It's not the type of weapon that matters here, but the rarity. If there were only 3 magic weapons in all the land, then needing a magic weapon to hit something would have the feel you're looking for.

We use "elements" in our home brew. I don't think we use them to the extent you do, since our home brew is really light, but each "effect" (magic spell, high-tech item, or steampunk invention) has an element that describes its modus operandi. We use: earth, air, fire, water, void, psionic, high-tech, supernatural, magic, and steampunk.

This works for a settingless system designed to be generic. But I think your answer is going to lie somewhere in your setting -- information we don't have yet. I'm thinking something like Zalman's comment about mythological weapons or Psikerlord's comments about how rare and fiddly the weapons should be.

A lot depends on how often this occurs. Is ever adventure going to be some variant of "find the ancient foes of your enemy and acquire the weapons they designed to destroy your enemy"?

QuoteI guess the sort of atmosphere I am going for is one where the heroes have to get the weapon they need from a particular smith, rather than having any old mage place a miscellaneous enchantment that works against anything. I just doesn't feel like the myths and fairytales that inspired fantasy, IMO.

I don't think you are going to have a single rational for why something works, as each enemy will/should be different. Unless you are trying to model the ability of the characters to create mythological weapons, just go with the smith/enemy/diety/whatever can create (is made up of or has collected) stuff that hurts your foe.