I've only found one (Other than a glitched rom of Gold which resulted in every Spinarak being shiny.) and it was a Tangela found on that tiny patch of grass between Kanto and the ocean leading to Cinnibar Island in SoulSilver.
A Carnivine that I just caught on Sunday during my lunch break at work. Totally unexpected. I was half asleep and heard that jingle and was wide awake real quick. I wasted my Master Ball cause my team would OHKO her.
Other than the Red Gyarados or anything from the Odd Egg in Crystal (50% chance of Shiny)? I remember the circumstances vividly; I was en route to my Secret Base on Route 120 (it's the one in the bush right by that little pond and the loamy soil, there's a Kecleon right by the entrance, and Registeel is quite literally right in the backyard) in Ruby Version, and I was traveling from Fortree. Back then, I would avoid all the tall grass I could, because the concept of using Repels never occurred to me. Between Fortree and my Secret Base, there's a way one can go so as to avoid all but exactly one tile of tall grass. I stepped into that one tile, and sure enough, battle. I groaned and rolled my eyes... and then I said to myself, "wait a minute... Zigzagoon have brown fur..." And sure enough, I saw stars swirling around a male Zigzagoon whose normally dark brown fur was red. After much celebration, I threw a single Ultra Ball, and the Zigzagoon was mine. I still have it to this day, but as I now have three Shiny Linoone, I don't know which one was the first. I mean, one of them I caught as a Linoone, in a Repeat Ball, I can rule that one out, but the other two are in Ultra Balls (the other one I also caught as a Zigzagoon, on Route 102, while EV training a Sudowoodo), they're all Linoone, all level 100, all of them currently in my Black 2.