It's the icon by the name in G/S/C (sparkles), the ring of stars that appears when it enters the battle, and I believe I heard a gleam sound effect when I encountered one in Sapphire (a Winggull with green stripes instead of blue, but I was looking away and I guess I never used it after I caught it). That cartridge is long gone.
Also, a big flash of light comes from the Pokeball in Stadium 2. Alt. Color seems to be the official term, and it makes more sense... I would call them either, or get specific. Example, I once had a black Hitmonlee with the move Dizzy Punch.