I love that part of it too! Though I always wondered why of all the themes to reappear in standard/hidden pits and maybe a few other places, it was that one.
On the subject of impending doom, shoutout to the Dodongo's Cavern theme! Especially the reorchestrated versions.
Mine probably is kind of popular, but Kokiri Forest always makes me feel warm and fuzzy inside. I also like how it subtly reappears on Outset Island in WW!