Arceus: Type Plates
Pikachu: Light Ball
Chansey: Lucky Punch
Ditto: Metal/Quick Powder
[email protected]: Soul Dew
Cubone/Marowak: Thick Club
Porygon2: Dubious Disc
Feebas: Prism Scale
Dusclops: Reaper Cloth
Swirlix: Whipped dream
Happiny: Oval stone
Kyurem: DNA Splicer
Landorus/Tornadus/Thundurus: Reveal glass
Palkia: Lustrous orb
Dialga: Adamant orb
Then there's obviously the mega stones for each respective mega Pokemon.
I think that's all of them now.
It looks like you missed a few (unless I overlooked them).
Rhydon- Protector Seadra- Dragon Scale Feebas- Prism Scale Giratina-
Grisceous Orb Porygon2- Dubious Disc
And if you count these Kyogre- Blue Orb Groudon- Red Orb Rayqauza -
commented 49 minutes ago by Sir_Mudkip (with additions from ShinyFire and ReadyAimFire)