My first shiny was a shiny Wingull on Sapphire version on Route 117 or whatever the DayCare is on. This was post game and sadly I couldn't trade him up, so I just trained him on there. Later on, I started up a Gold version and eventually found an Abra outside of Goldenrod. It fled, but I really wanted an Abra, so I went to look for another and found a shiny Nidoran F. She was most definatly used on that team. I've also found many shines in hack games(chinchu in Dark Rising, Surskit on my main team in Reign of Legends, Rattata on my team in Dark Energy(first encounter o_O didn't know it has boosted shiny encounters. XD), and Machop on Rescue Rangers WHICH OF COURSE I HAD NO POKEBALLS ON) but as you said hacks don't count.
Currently I'm trying to Masuda breed a Marill in Y, so sorry if get wonder traded a level one marill from Al. :P