The Gastly line are made of poisonous gas.
The Misdreavus line might be an exception. My best possible guess for what it's body is made from is that the jewelry and clothing motif in the line could point to them being made from those objects.
The Shuppet line has Banette being a throw away doll or puppet, and Shuppet being a puppet or made from materials used to make doll and puppets.
The Duskull line is made from things like bandages which are seen on Dusclops, the reaper cloth could be part of Dusknoir body, The spectral ball of fire mentioned in the Pokedex entries for Dusclops, which could be the single eye found on each member of the line, and maybe even actually bones considering Duskull having a skull along with bone marking on it's back.
The Drifloon line are balloons
Spiritomb is 108 spirits bound to an Odd Keystone, although I'm not sure if Spiritomb was a Pokemon made from 108 spirits that later was bounded to an Odd Keystone, or if the 108 spirits being bounded to an Odd Keystone was what originally created Spiritomb.
The mask Yamask has and the coffin Cofagrigus is in could be part of their physical body, although I'm not sure then what the rest of the body is made of. Galarian Yamask and Runerigus are a similar deal but with clay instead
The Jellicent line are made of seawater, as stated in their Pokedex entries
Female Jellicent
These Pokémon have body compositions that are mostly identical to seawater. They make their lairs from sunken ships.
Male Jellicent
Most of this Pokémon’s body composition is identical to sea water. It makes sunken ships its lair.
Both of these entries are from Pokemon Sword.
The Litwick line, Litwick is a candle, Lampent is a lamp, and Chandelure is a chandelier.
The Honedge line are possessed swords
The Phantump line, Phantump is a possessed stump, and Trevenant is a tree
The Pumpkaboo line are pumpkins. The Pokemon Shield entries for Gourgeist mentions it being able to pass on it's size to it's descendants, which could be evidence towards this theory.
Small Gourgeist (The Pokedex entries for all other sizes except for average size are similarly written)
A small-sized Pumpkaboo evolves into a small-sized Gourgeist. Its bodily proportions also get passed on to its descendants. From Pokemon Shield.
The Sandygast line are made from sand
Dhelmise is made from seaweed, a steering wheel, and an anchor.
The Sinistea line is made from tea inside of a teacup or teapot
Galarian Corsola, and Cursola are made from what might be it's body from when it was alive, and ectoplasm. Ectoplasm could possibly be a part of the bodies of some other ghost type Pokemon.
The Dragapult line could be another exception, although it might be partially made from the fossil it left behind after originally dying.
The Bramblim line is made from dried grass
The Greavard line could be something like a zombie, especially considering Houndstone looks like a skeleton.
Gimmighoul is a coin that turned into a Pokemon as stated in it's Pokedex entries
Roaming Form
This Pokémon was born from passion that seeped into a coin. It wanders, apparently seeking to return to the treasure chest it once inhabited. From Pokemon Scarlet.
Goldengo body is made from coins