There are hundreds of Pokemon specific items and it would be a monumental task, so I will just write the families with special items.
Bulbasaur
Charmander
Squirtle
Pikachu
Clefairy
Jigglipuff
Meowth
Hitmon-Family
Chansey
Mr Mime
Scyter
Jynx
Electabuzz
Magmar
Lapras
Eevee
Snorlax
Aticuno
Zapdos
Moltres
Mewtwo
Mew
Chickorita
Cyndaquil
Totodile
Togepi
Marill
Sudowoodo
Wobbuffet
Sneasel
Teddiursa
Mantine
Raikou
Entei
Suicune
Lugia
Ho-Oh
Celebi
Treecko
Torchic
Mudkip
Skitty
Plusle
Minum
Castform
Regirock
Regice
Registeel
Latias
Latios
Kyogre
Groudon
Rayquasa
Jirachi
Deoxys
Turtwig
Chimchar
Piplup
Bidoof
Shinx
Pachirisu
Buizel
Cherubi
Drifloon
Spiritomb
Gible
Lucario
Rotom
Uxie
Mesprit
Azelf
Dialga
Palkia
Heatran
Regigigas
Giratina
Cresselia
Phoine
Manaphy
Darkrai
Basically they can have between 1 and 12 special items each, so there are way to many items to list them all.
Source: http://www.serebii.net/dungeon2/croagunk.shtml