This is a comprehensive list of suggestions where the new damage types can be implemented in various spells, attacks, and creatures in-game. Everyone is more than encouraged to contribute ideas.
Ballistic- Barbarian Damage Immunity: Should include Ballistic.
- Barbarian Perks: Gladiator, Huscarl, and Nomad perks should alter Ballistic immunity.
- Sorcerer Perks: Bouldermancer should gain Ballistic immunity. Scion should gain Ballistic resistance. Hematologist should gain Ballistic immunity.
- Fighter Perks: Man-at-Arms, Executioner, and Dual-wielder perks should also gain Ballistic immunity. Man-at-arms activated feature should also include Ballistic.
- Rogue Perks: Thugs should gain Ballistic resistance.
- Entropic Shield: Should also grant 20% immunity to Ballistic damage.
- Stoneskin: Resistance should include Ballistic damage.
Poison- Beings who are immune to poison should be immune to Poison damage.
- The poisoned status could inflict Poison damage every round. 1d6?
- Healing Sting: Should be changed from Negative damage to Poison damage.
- Quillfire: Should be changed from Piercing damage to Poison damage.
- Cloudkill: Should be changed from Acid damage to Poison damage.
Bleed- Beings who are immune to critical hits/sneak attacks should be immune to Bleed damage.
- Dying: Should be changed from Magic damage to Bleed damage.
- Resting: Automatic HP adjustment on canceled rest should be changed from Magic damage to Bleed damage
- EFUSL: Automatic HP adjustment on login should be changed from Magic damage to Bleed damage
- Wounding: Should be changed from Physical damage to Bleed damage.
- Drowning: Should be changed from Magic damage to Bleed damage.
- Executioner Fighter Perk: Level 8 bonus should be changed from Slashing damage to Bleed damage.
- Keen Edge: Could grant +1 Bleed damage.
- Drown (Spell): Should be changed from Magic damage to Bleed damage.
- Extract Water Elemental: Should be changed from Magic damage to Bleed damage.
Astral- Starblight: Should be changed from Magic to Astral damage.
- Stellar Blade: Should be changed from Magic to Astral damage.
- Burst of Radiance: Should be changed from Magic to Astral damage.
- Star Shard: Should be changed from Magic to Astral damage.
- Lunar Bolt: Should be changed from Magic to Astral damage.
- Solar Circle: Should be changed from Magic to Astral damage.
Psychic- All summoned creatures in the Astral theme should have their bonus Magic damage and bonus Sonic damage replaced with Psychic damage.
- Sorcerer Perks: Nightmare should be changed from Magic to Psychic damage.
- Curse Song: Should be changed from Sonic to Psychic damage.
- Vicious Mockery: Should be changed from Sonic to Psychic damage.
- Wounding Whispers: Should be changed from Sonic to Psychic damage, especially the GSF Evocation benefit.
- Clarity: Could provide absorption against Psychic damage, akin to Protection from Elements, ending early if overwhelmed.
- Illykur's Mantle: Should also provide 10/- Psychic damage resistance.
- Phantasmal Killer: Should be changed from Magic damage to Psychic damage, for both partial effect and death effect.
- Mind Fog: Should inflict vulnerability to Psychic damage on a failed save.
- Feeblemind: Death effect should be changed from Magic damage to Psychic damage.
- Lesser Mind Blank: Could provide absorption against Psychic damage, akin to Energy Buffer, ending early if overwhelmed.
- Mind Blank: Should provide immunity to Psychic damage, akin to Negative Energy Protection.
Crushing- Failed Climbing Checks: Should be changed from Magic damage to Crushing damage.
- Failed Boulder Lift: Should be changed from Bludgeoning damage to Crushing damage.
- Gust of Wind: The GSF Evocation benefit should be changed from Magic damage to Crushing damage.
- Heart Clutch: Should be changed from Negative damage to Crushing damage.
- Evard's Black Tentacles: Would make sense, but would be massively overpowered due to Crushing damage penetrating immunities.
- Future's Pain: Should be changed from Bludgeoning damage to Crushing damage.
- Gravity: Should be changed from Magic damage to Crushing damage.
- Collapsing Void: Should be changed from Bludgeoning damage to Crushing damage.
Earth- Earth elementals should have On Hit: Earth Damage, akin to the damage bonuses of other elemental types. This might require a proportionate adjustment of other stats for balance.
- Djinn of Earth and Flesh should have their Acid damage replaced with Earth damage, where relevant.
- Endure Elements/Resist Elements/Protection from Elements/Energy Buffer: Should protect against Earth damage, like it does other elemental effects.
- Sand Splash: Should be changed from Piercing damage to Earth damage.
- Sand Pillar: Should be changed from Piercing damage to Earth damage.
- Call Lightning: Cavern effect should be changed from Bludgeoning damage to Earth damage.
- Cone of Stone: Should be changed from Bludgeoning damage to Earth damage.
- Sand Storm: Should be changed from Piercing damage to Earth damage.
- Earthquake: Should be changed from Bludgeoning damage to Earth damage.
Everything- Commander Rogue Perk: 1% damage immunity should include Ballistic, Poison, Psychic, Crushing, and Earth. Intentionally not including Bleed and Astral.
- Glass Doppelganger: Should be resistant to Psychic, Poison, Bleed, Earth, and Ballistic, but vulnerable to Crushing damage.
I'd suggest adding Force, to move things off of the 'Magic' damage category, and saving that just for when unavoidable damage needs to be applied.
Force
Magic Missile
Issac's Lesser Missile Storm
Isaac's Greater Missile Storm
The various Bigby's spells
Devastating Body Swap
Disintegrate
Gravity
As well, the Energy Blast spell might need updating to have new types. And the Orb spells might benefit from being made one spell with subspells, ala Enhance Ability "Elemental Orb"