This is just for the Pokemon's sprite, some Pokemon might be holding items in fan art, in the anime, and other places.
The following list of Pokemon are holding something in their hands.
Hypno is holding a pendulum.
Cubone is holding a bone.
Marowak is holding a bone.
Farfetch'd is holding some sort of stick/onion.
Timburr is holding a plank of wood.
Gurdurr is holding an iron bar.
Conkeldurr is holding two concrete cylinders.
Braixen has a stick in it's tail.
Flabébé is holding a flower.
Floette is holding a flower.
Honedge is holding a sheath.
Doublade is holding two sheaths.
Aegislash (Blade forme) is holding a shield.
Kadabra is holding a spoon.
Alakazam is holding two spoons.
Mega Sableye is holding it's giant gem.
The following list of Pokemon are holding items on their Pokedex page art.
Delphox is holding a stick.
Hoopa is holding a ring.
Delibird is holding a sack of food or something.
The following list of Pokemon are not exactly holing items, but still have them on their body.
Chansey's egg in its pouch
Braixen's stick in its tail.
Meowth's charm on its head.
Mega Alakazam's spoons that it is levitating.
Togepi has half of an egg shell on its stomach.
Slowking's crown on its head.
Blissey's egg in its pouch.
Samurott's swords and armor.
Zoroark has some sort of bead or hair tie on its "mane."
Hitmonchan's boxing gloves.
I think I got them all, tell me if I missed any.
Hope this helps!
Source (I just scrolled through it.)