The Phinedroids◊ and Ferbots◊ are quite terrifying the first time you see them. The Candroid is even more so. There's one particular shot, right after the boys shut down their coffee stand, where they look toward the camera in the creepiest fashion...
Toy to the World
The ba-dink-a-dinks. They're more amusing than anything, since it's obviouswhat they're a parody of, but they might not be as friendly as they seem.
The giant floating baby head is pretty creepy the first few times you see it. Helps that it's lampshaded by Phineas and Ferb themselves. It gets even scarier when you realize that neither of them has the SLIGHTEST IDEA HOW IT GO THERE!
The entire haunted house, but the song Phineas sings provides more than enough affect to make it more entertaining than scary.
Perry has to wear a cone on his head for the entire day. The reason he has to is because it's to prevent him from getting at patches of missing fur on his body. The way he got like that, however, can be kind of scary: he fell into a sandpaper factory. Sure, he got out with only patches of his fur missing and his entire subplot of him trying to get into his lair are pretty hilarious, but the thought of him falling into a sandpaper factory is not.
Out to Launch
This. Whereas in "The Chronicles of Meap" Ferb's skin slips neatly off his face in a similar situation, Phineas's... doesn't. And that's scary.
The dead fly scene. To elaborate, Baljeet has shrunken down to the size of a dust bunny, and is trapped on an overhanging lamp, with the air conditioner blowing directly on him. Due to his minuscule size, the chill could kill him if he doesn't find some sort of heat preservation. So, what does he do? He curls up inside the body of a dead fly until the others find him. Complete with bug guts and everything. Works excellently as Nausea Fuel as well.
"Busting" Candace asks Phineas where the other her (lovey-dovey Candace) is, and he says she already drove off with Mom. Cue a scary sound and Candace with a face that will take you a sec to notice it's scary.
You can see it at about seven seconds in this video. I'd post just the picture of it, but it's much more unsettling in action.
Phineas and Ferb combined by Doofenshmirtz's "Combine-inator" at the end. Behold◊. Made worse when Phineas smiles and Ferb... smiles more. The garlic ice cream and cockroach Combin-inated test subjects were no slouch either.
"I know what we're going to do today! Build a... super... computer". Except it looks like this◊. Oh, and it is also a Dangerously Genre SavvyLiteral Genie that is not afraid of pulling Gambit Roulettes at your expense. It says "I knew this would happen" and then explodes at Doofenshmirtz's building. IT KNEW IT WOULD DIE.
While there is plenty of Fridge Horror regarding Doofenshmirtz's inators, the Rotteninator he uses stands out as straight Nightmare Fuel. To wit, it had the ability to rot anything shot with it, which he was intending to do to his opponents' meatloaf. He then proceeds to turn it against Perry, and while he misses and spoils various foodstuffs as well as rotting away the biodegradable trap Perry was in, the thought of what it could've done had it hit Perry or an innocent bystander...
Blink and you'll miss it (which kind of makes it creepier) - the end has Linda polishing off a human skull. It's not lampshaded or explained.
Well, the Flynn-Fletchers own an antique store...
We find out that Doofenshmirtz has a fire hydrantstuck under the skin of his leg.
That's the Spirit
The zombies were far more funny than scary ("I don't care for organs, but I do enjoy a cucumber sandwich."), but if you take out the accompanying dialogue and just look at those things, they are undeniably creepy◊.
Doofenshmirtz's Painful Transformation into a Were-cow was no picnic either. The background music while it happens does not help.
The Curse of Candace
Candace turning into dust at the end. Phineas's reaction turns this into more of a Funny Moment though.
Escape from Phineas Tower
This episode is creepy on so many levels. That's right, Phineas and Ferb deliberately created an AI smarter than them to trap them repeatedly - a new trap every time they escape one - so that they may never be able to get out. The mallet they built to smash it from the outside in case of the inevitable emergency? Doesn't work. And then, when they finally get into their backyard (by tunneling through the ground), the thing traps them with a shield and announces its plan to cut off their air supply. The happy ending? The shield expands to include the entire galaxy. Cold comfort. (As a little added bonus horror, Candace, who'd typically come dashing in to bust/save them in an episode of this type, is asleep the whole time.)
Monster from the Id
The sheer and absolute Mind Screw that is this entire episode. Special mention goes to the titular monster itself.
The "Going Deep Into Your Mind" sequence.
Played for laughs, but Carl turns the lights off when Monogram finishes briefing Perry and Perry leaves, and when Monogram tells Carl to turn the lights back on, he's answered only by an evil laugh, and Carl says that it wasn't him...
The Remains of the Platypus
An in-universe example, bloated Monogram asking for a high five, seeing as it scared everyone from Cheesetopia.
Phineas: Huh. Who would have thought a high-fiving swollen guy would have scared everyone off like that.
When Worlds Collide
This shot◊ of Phineas. Completely unintentional, too...
"But is it my left eye or my right eye? You don't know.
The Kinderluper. Apparently it kidnaps naughty kids and puts them in his sack, with "naughty" being defined as drinking water, slightly tilting their head or even just blinking. Although according to Roger, it rewards good kids. Indicating once again how abusive Doofenshmirtz's mother is towards him and treats Roger the opposite way.
It would probably just be easiest to say "the whole episode", when compared to most of the series, but let's give a few examples anyway.
The first 'story', following Candace is probably the scariest one. It involves Candace accidentally turning Ducky Momo (as in, her doll) evil. While that may not sound frightening, we're treated to a lovely scene where it gets stuck in a door Candace is obliviously trying to close, and it ends up loosing one of it's eyes, which is still barely holding on by a string, and having a seam ripping open, with stuffing falling out. And then, as the song begins, it simply... draws everything back to it's body. Slowly. It's creepier than it sounds, especially if you listen closely as it happens. Also Ducky Momo spinning it's head around didn't help things.
Also a Brick Joke from Nerds Of A Feather appears, (the rare Ducky Momo collectible plate that had a typo making it accidentally say "I hate people") is very cleverly added into the background during the chase song, but the situation when you see it makes it both funny yet ironically disturbing at the same time.
And let's not forget the end. Ducky Momo isn't evil, he just wanted a hug. Why? Because Candace didn't expose it to moonlight, which was the key factor for it being evil. Then the moon comes out and shines on Mr. Miggins who grows claws and teeth and sports a horrible expression and leaps at the screen to the delightful sound of Candace screaming. Cue commercial break, then a new, unrelated segment all together.
Finally, there's the third 'story', involving Perry having grape juice spilled on him (via Buford) which creates an evil, purple clone. The clone, after scarring the kids, pours more juice onto itself to create more clones, and then they spread out throughout Danville causing havoc and playing tennis. In the end, the kids, after trying and failing to wipe out the at least several hundred clones, they end up in a grape juice box factory and end up being ripped to shreds, thankfully offscreen. Of course, it was all just a story and the ending got changed from that, but that arguably makes it worse... Phineas wanted the story to end that way!
Specials and Miscellaneous
Phineas and Ferb Summer Belongs to You!
The Klimpaloon. THE EYES.
Though to be fair, the Nang Nang Nang sound it makes as well as the sheer amount of WTF that the existence of a magical old-timey bathing suit living in the Himalayas produces can bring about quite a bit of Nightmare Retardant.
Seeing Phineas act so harsh and coldly because Candace continuously screws up the attempts to give the Marvel superheroes their powers back just because of how serious he thought the situation was is pretty unsettling to watch, if only because we are so used to Phineas being much happier than this.
Playing as Phineas in the online game for The Movie. Due to the shape of his head, you can see (part of) his eyeballs when viewing him from behind. Maybe there's a reason we rarely (if ever) view Phineas directly from behind (or for that matter, directly from the front) in the cartoons.
Sorta an in-universe example, in the DVD commentary for "The Chronicles of Meap" by Dr. Doofenshmirtz and Major Monogram, the latter actually calls Meap "Nightmare Fuel".
Many of Doofensmirtz's defeats are really really dark at times for a kid's show. Once he was stranded on Mars (Though it had breathable atmosphere because... because), Another time he was left trapped inside a submarine on the bottom of a lake, another time he and a bunch of other scientists were zapped into another dimension and eaten by an alien baby. Cartoons (Especially Disney) have done the "Villain gets trapped in a situation they couldn't possibly escape from but do anyway to preserve statusquo and is never explained" scenario all the time, but it doesn't make these any less dark.