Ahh, yes, this means I was thinking along the right lines then last night after I'd gone! I was thinking about the Great Fairy queen, how she sends out those two fairies, and she's in multiple games... but anyway, on to the current riddle
Hrrrm... I never finished FSA (lazy brother never plays with my on our supposedly joint game), but let's think... ... ... ... I can't think of anything specific enough, I'd've said either level bosses or the dark orbs you have to smash at the end of a level... or perhaps the deku scrubs in the Lost Woods there... but they appear in other games too... hmmmm...