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Red Gyarados from Lake of Rage, but since that's a common and uninteresting one:
One of those guys in the Rocket Hideout was shiny. I didn't know what a 'shiny' was back then (or that the Red Gyarados was one and other Pokemon could be a different color as well) but since it looked different, screen lit up intensely (for kid-me that was pretty intense) and sparkles appeared around it I knew this one must be special. Couldn't catch it though, sadly.