Deoxys, in the Delta Episode of Omega Ruby/Alpha Sapphire, and Celebi, after defeating Red in Crystal.
Update for Crowned Tundra, HOME, LGPE, and USUM:
Keldeo can be obtained after capturing Virizion, Terrakion, and Cobalion on a small island with a cooking pot in the water by the Dyna tree hill. You have to cook with the three Pokémon mentioned earlier and Keldeo will spawn.
Magearna can be obtained in SM by scanning one of these QR codes.
Magearna can be obtained in USUM by scanning one of these QR codes.
Magearna’s original form (a different coloration, but not a shiny) can be obtained in Pokémon HOME by having had every Pokémon in the game at one point.
Mew can be obtained via the Pokeball Plus in LGPE.
Jirachi, Shaymin, Darkrai, and Arceus can be obtained using glitches.