I have to give it to the Guardians of the Silent Realm, Skyward Sword.
Why?
Because no other enemy inspires that pants-ruining feeling like these guys do.
Of course, they are not the only enemies that inspire that "oh crap" feeling. I mean, remember how you reacted the first time you saw Ganondorf transform into Ganon in Ocarina of Time? And yes, the infamous Wallmasters/ReDeads will still freak you out a bit, don't they?
So what makes the Guardians so special?
You are powerless against them. With every other enemy in the series, you have the advantage. You have your weapons, so they aren't as much of a threat--just smack 'em a couple times, and skip away happily. But with Guardians, you do not have your weapons. You don't have your sword, or your bombs. The only thing you can do is run, very very fast. If you're not close to a Tear of Light (or whatever they're called), you are in some serious trouble. Furthermore, even if you GET a Tear thingy, they are still an ever-present threat. Between the 90-second timer, the Walking Water (or whatever it's called), and those lantern-carrying ghosts, you are not safe from them.
Long story short, the Guardians are frightening enough as it is, but the simple fact that you are powerless against them makes them my personal favorite Zelda enemy.