Maybe clones as well.
I don't think Peter's been scared of Venom since the 90's ended.
Well Peter isn't scared of Juggernaut, and in the case of Firelord desperation overcame fear, and Peter probably has a "What doesn't kill me makes me stronger" attitude after them.
But Doom is someone Peter has tussled with and never won, and each time Doom could have killed Peter easily. So that's a different kind of fear.
True, Doom is one of the few people in the Marvel Universe that is more powerful than Peter in every way. Like usually, when he's up against someone more physically powerful than him (Juggernaut, Firelord, etc.) he holds a huge intelligence advantage, but in terms of Doom, he's outgunned and out of his depth.
"Anyone can win a fight when the odds are easy! It's when the going's tough - when there seems to be no chance - that's when it counts!" - Spider-Man
Peter is scared of everybody, but he doesn't have a pathological fear of anyone. At least, not anymore.
That being said, hatred and fear are naturally intertwined so the villains that Peter fears/hates most would have to be Red Skull, Green Goblin, and Morlun.
That's a good point. Yeah, Jugs and Firelord are not as sharp as Peter so that gives Spidey a competitive advantage.
Doom though has awesome tech, he's also a master sorcerer, he's a genius in science/military/politics, and he's also a great physical combatant and knows martial arts. I always saw him as evil Batman or evil Bruce Wayne in the sense that he's good at everything and is always able to do the prep time.
So Spider-Man has no advantages against him.
Yeah, in some ways Doom is Batman turned up to 12 what with the gadgets, magic, and even how he's supposedly a skilled martial artist.
"Anyone can win a fight when the odds are easy! It's when the going's tough - when there seems to be no chance - that's when it counts!" - Spider-Man
The difference is that with Batman there's always something ridiculous about him beating Darkseid with prep time as "his followers on the internet" (as Brainiac would have it) says.
With Doctor Doom, you can totally buy it. This is the guy who's made Ultron, the Beyonder and others his B-word, and he did that to Galactus (twice).
Doom is my favorite Marvel character after Spider-Man, and somehow it never bothers me when Doom kicks Spidey's a--. I'd love for there to be a day when Spider-Man gets a win, but it has to be the greatest Spider-Man fight of all time and it has to be a clear convincing clean win.
Green Goblin for obvious reasons.
Venom apearences had estabilished especially in the first stories how he is a scary villain to Spider-Man.
I want to say Carrion as well,because he is one of the first villains that powers and visual are quite scary.And he is a villain that apeared way earlier that the scary villains so to say from the more edgier comics books from the late 80´s and early 90´s as Demogoblin or Carnage.
Peter’s greatest fear is not a fear of a super villain it is a fear of failure. He knows he failed Uncle Ben, Captain Stacy and Gwen, which is why he has been unable to get over them. Conversely, In my all-rime favorite issue, ASM 33, his fear of failing Aunt May ( like he did Uncle Ben), kept him going and gave him perhaps his single greatest victory.
Out of all the times they fought Darkseid, Batman killed him that one time. That's it. And internet fanboys blow it up.
Because when Anti-Monitor, Imperiex, Superboy Prime or Megaddon showed up....where was Batman? He didn't do crap against those guys. So he's still skillfully inept if you look at the overall picture.
Doom can beat anyone, and do anything....but that's his character ever since the beginning.
Oh yeah, Batman is like the definition of power creep and it honestly has affected my views on the character overall.
Doom, on the other hand, was always on that level, which is why it doesn't bother me when he does ridiculous things. And I'd definitely love for Peter to get a win sometime, but as you said, it needs to take all his intellect and willpower for him to outsmart and outlast someone like Doom. It could make for a really epic 4/5 issue story arc, come to think of it.
"Anyone can win a fight when the odds are easy! It's when the going's tough - when there seems to be no chance - that's when it counts!" - Spider-Man