Bosses that make you cringe (Not for the faint of heart.....or little kids.)

[miltankRancher]

Nemesis from Resident Evil. He is the scariest villain from my childhood. Evil cousin of mine. :\

also, Chaos in Dissidia and Duodecim is pretty hard to beat. But his design is suckish.

 

[Masterge77]

Marx Soul from Kirby Super Star Ultra, need I say more?

 

[Sydian]

Redeads from Zelda take the cake. They are worse than bosses. As far as bosses go though, Big Daddies from Bioshock, that guy with a lot of faces in FF13, Masked Man in Mother 3, Gohma in Ocarina of Time, just to name a few. Big Daddies are freakin' scary, guy with a lot of faces whose name I can't remember took me too damn long to beat and he's creepy, Masked Man is the saddest fight in gaming history imo and Gohma...well it may be the first boss in OoT, but still, that doesn't make it less creepy.

 

[Gold19]

I'd have to say the SA-X from Metroid Fusion. Good god when that thing entered the room that your in as well, the music just turned sinister and evil (including the chase scenes).

 

[Cherrim]

I played Nier recently and was very, very put off by Halua (Weapon 6). The battle itself was almost ridiculously easy but I found it really hard to do simply because the boss's appearance was really unsettling. D:

Also that one boss from under the well in Ocarina of Time? Still creeps me the hell out when I see screenshots of it. :(

I think that's really about it, though. Some bosses will make me cringe because they're really hard or they're annoying fights, but these are the only two that really pop into my head when I think of bosses that made me really uncomfortable.

 

[TRIFORCE89]

Also that one boss from under the well in Ocarina of Time? Still creeps me the hell out when I see screenshots of it. :(

:p

Dead Hand is all the better in 3D too.

Aaaanyway, I don't think I've played many games with creepy bosses. I can't really think of any. Enemies, sure. Bosses, not so much.

So that I have an answer, I'm going to go with Majora. It's not scary in appearance; it is just a mask after all. It's a different kind of scary. Twilight Zone kind of creepiness.

 

[Kung Fu Ferret]

Definitely Andross's Brain in Star Fox 64. I never beat it, even on the 3DS. One, it was uber hard, Two, it always gave me the creeps.

 

[U.Flame]

Dead Hand is all the better in 3D too.

I think differently. It still retains it's creepy smile and freakishly long mouth, but they took out all the blood stains. It's just...pale now. Really boring. I like the original bloody version.

 

[TRIFORCE89]

I think differently. It still retains it's creepy smile and freakishly long mouth, but they took out all the blood stains. It's just...pale now. Really boring. I like the original bloody version.

Did they really? I don't remember that. Well, darn. I remember the hands being in 3D to be rather cool though.

 

[Nash Bandicoot]

This may not be considered a scary boss, but the big jack-in-the-box in Donkey Kong 64, that was scary as a kid. It didn't help that it was also quite a tough boss back in the day. But nowadays I don't think it's annoying and I love it. :D

oh, I had never seen that before but it win's, that's scary...
The scariest monster/enemy would be in Far Cry, these monster things with Rocket Launchers attached to their arms, when I was little they scared me heaps.

 

[Chairman Kaga]

Did they really? I don't remember that. Well, darn. I remember the hands being in 3D to be rather cool though.

They baby-fied Dead Hand in OoT3D? That's depressing.

In the scary department, pretty much any boss from Demon's Souls, but Adjudicator and Maneater especially. Black Skeleton is more terrifying than any of them, though, and he's just a regular enemy, heh.