A shiny Ratatta outside Pallet Town in Silver. It was way, way after I finished the game and I just liked to roam around, filling my pokedex the most I could (since I didn't know anyone with a GB to trade with). I wasn't really paying attention, so I didn't see the shiny intro, but since it was a little lighter in color than usual, I decided to catch it.
Years later, in Emerald, I caught a Shiny Oddish outside the Safari Zone. Once again, I wasn't paying attention, but noticed it was green instead of blue. I couldn't remember if normal Oddish were green or blue, so I decided to catch it.
In Pearl, I caught a Shiny Onix in the Victory Road. That one I did see it's shiny intro.
Then in X (my last Pokemon game), I got a Shiny Aerodactyl from the amber you get in the story, and accidentally killed a Shiny Hoppip when EV training a Blastoise (Selected Surf instead of another Water attack) outside the Daycare.