I've caught more shinies in X than I can think of right now. @_@ So I'll just recount the ones from Gens 2-5.
Crystal:
Igglybuff, from the Odd Egg. I never realized it was shiny until years later, I thought the sparkles were because it was a special Pokemon, being hatched from an egg.
Girafarig. I killed it, because I thought the blue nose meant it was sick and I couldn't run away from it. ;A; Stupid 11 year old logic!
Firered:
Zubat, Also killed it. I knew what shinies were at this point, and tried to catch it. Apparently the move I used was too strong, since it fainted. D:
Soulsilver:
A Vulpix, while I was grinding outside the Safari Zone. I actually caught him! Named him Silva, evolved him, and traded him up through to Generation 6.
I never encountered any shinies in R/S, D/P, or B/W. I caught the Red Gyarados in SS, and the shiny Haxorus in the Nature Preserve, but I'm not counting them.