I've found these shinies in the third gen:
Wingull, Charmander, Eevee, Rayquaza, Porygon, Treecko, Mewtwo, Latios, Dratini, Torchic, Scyther, Registeel, Mudkip, Latias, Bulbasaur, and Squirtle. That's it's...for now.
My cousin has found a shiny Skarmory, and my brother has found a shiny Vulpix and Rattata in the third gen as well. My cousin traded me the shiny Skarmory. My brother originally caught the shiny Vulpix (he evolved it, in case you're wondering), but it was deleted by my cousin out of jealousy, and the shiny Rattata was one that he saw before he had any PokeBalls at the beginning of the game (he started a new game a few months after his shiny Ninetales got deleted).