For me it's probably Queen Gohma.

As a kid, this scene right here nearly made me wet myself. I remember making my sister fight her for me because I was just too scared. I had many chances to fight the battle on my own, but I never could summon the courage.
ReDeads are a close second, though I guess they dont count as bosses. That sound! That...freaking...sound...! ugh. *shivers*








