When I lost my SS, I lost 90% of my pokemon. Currently i'm playing Emerald/My sister's Pearl.
I have no shinies on Emerald currently, as I transfered my only one to Pearl.
On Pearl I have JPN Crown Beasts, ENG Raikou and Entei, a PCP, Mightyena, Metagross and Flygon. I believe that's it.
The only one of those I got myself was Mightyena in Emerald, very early in the game. I don't know if you would count PCP as shiny but...whatever.
I have seen many other shinies. Two from the top of my head (excluding Gyarados in GSC/SS) are an Ekans in Silver, which sadly has a fried memory chip doohickey (yes, I said doohickey. Oh well :P) and a Lickitung in SS in the Safari Zone, which fled. I have seen more but can't remember them all.