Groudon, Kyogre, Regiice, Regirock, Registeel, Latios or Latias and Rayquaza. Jirachi and Deoxys are obtained in a special way, Google search it
Latios is not catchable in Sapphire you must get one from Ruby or Emerald.
Squirtle is not catchable in emerald.
Surskit is NOT catchable in Emerald. Trade from Ruby/Sapphire.Of course you can get a surskit: just run around in the grass at rout 102. They're kinda rare though.
Unowns are only catchable in firered and leafgreen trade one to emerald to have it.
zapdos, moltres, articuno, mew2, and all Legendary Pokemon in Gold/Silver/Crystal and Ruby/Sapphire/Emerald but only catchable ones are the first four listed.
*Mew is not catchable in Pokemon x and y, but you can get him online from wondertrades and such. Mewtwo however, is catchable and you can find him in the cave in pokemon village.
Poliwag is not catchable in Ruby, Saphire or Emerald.
Ditto.
rayquaza
Pokemon snap or Pokemon emerald
sudowoodo and smeargle
There is no official Pokemon game that has all Pokemon catchable in it, which means you'll have to trade and transfer Pokemon from other games to get all the Pokemon. However, some fan-made hacks do have all the Pokemon catchable in them.