Anybody remember WPIX’s “Chiller” opening?
Used to freak me out just a bit when I was a wee lad in upstate New York.
“Meow!”
The Lynch/Frost logo was a little creepy, but that’s probably due to it coming at the end of “Twin Peaks”, which was kind of freaky itself.
“You have six fingers on your right hand. Someone’s been looking for you.”
The one I always think of immediately is the very first one in the OP’s link (Viacom). The loud synthesized music, the scary drums, and the “V” coming right at you always scared me. I used to love the PBS one, though.
No logos frightened me, but Metal Sonic’s voice in the Sonic OVA scared me for life.
“Gabby! GABBY, NO!”
There’s something a little oddly dark in some of the music, I admit–I’m not smart enough musically to say, but minor key maybe? In any event seems an odd choice for an advertising product.
Is that the one with the hammer and chisel? That one always startled me when I was a kid.
I saw the thread title and said, “Finally someone else knows what I’m talking about!” and then realized that someone was me from four years ago.
Not scary, but I hate hate hated the Thames logo that came on before, I think Ducktails or Richie Rich or something.
I can remember muting it or changing the station for a few seconds. I don’t know why but I it really bugged me.
I was there, and never thought them scary.
And the best were Mark VII Limited and MTM.
You’re definitely not alone. There was even a short documentary about it based around the Screen Gems outro: The S From Hell.
This, in my case, never failed to unsettle me right before the Muppet Show.
I never thought of them as scary before, but I can see how the one at about 0:016 might be.To have what looks like the word DIE coming at you in big yellow letters? Scary!
OK, the Taki Corporation after the Sonic OVA kinda scared me, but that was because of Metal Sonic. I couldn’t get his voice out of my head, and it creeped me out. Same thing with the ADV logo.
“THERE IS ONLY ONE SONIC…” 
That’s some bad hat, Harry!
I was scared by a lot of stupid harmless stuff on TV as a kid, and production logos were no exception…
When I could stay up to watch reruns of Barney Miller, the logo at the end (Four D Productions, I think?) had this eerie digital piano/door chime riff, but what I thought was really off-putting was the little sharp stinger note at the end. It was combined with this- how can I describe it? - flash in the corner of the screen, like the little circular spot they used to put in old movies to indicate the end of a reel, which was out of sync with the note by a half second or so. That kind of freaked me out.
The old Columbia Pictures starburst logo from the late 70s/early 80s (the one sitting in the middle of a semicircle), combined with some very WGBH-esque synthesizer music. I didn’t know what that was supposed to be; I suppose at the time I thought it was like a cartoon dynamite blast (minus the comedically oversized “BANG!” wordmark, of course).
The MGM logo. I wasn’t scared by the lion, surprisingly. What I was scared by was that little red mask with the black eyes and mouth sitting below the lion. What the hell was that supposed to be? A clown? A Mexican wrestler? A Zulu warrior? The illegitimate spawn of the ghost forms of the dragon and the balloon from Dig Dug? Three decades and change later, and I still haven’t figured it out.
I remember that from Dumb & Dumber 
I see I’m not alone in finding something unnerving the Mark VII chisel & hammer as a child. Part of it I think was that image, and part was that, at that time, I was too young to know Roman numerals and “Vii” was therefore a strange and unknown word. What did it mean?