Deoxys - Meteorite
Found in Professor Cozmo's house in Fallarbor Town.
Rotom - Household Items
Found in Professor Birch's Laboratory in Littleroot Town.
Giratina - Griseous Orb
Found on Route 130.
Shaymin - Gracedia
Found in the Berry Master's house in Route 123.
Note: You need to show a NPC a Shaymin first.
Tao Trio - Reveal Glass
Found in a mirror shop on the left side of Mauville City's main area.
Note: You need to show a NPC a Thundurus, Tornadus or Landorus first.
Kyurem - DNA Splicers
Found in the Gnarled Den (Kyurem's capturing spot) with the Dousing Machine towards the left side of the cave.
Keldeo & Meloetta - Secret Sword & Relic Song
Found in Crooner's Café in Mauville City.
Note: You need to show a NPC a Keldeo or Meloetta first.
Genesect - Drives
Found in Mauville City.
Furfrou - Pretty Hair Trims
Found in the Pokémon Fan Club in Slateport City.
Source! My bad if I missed any!