I don't think any villain has ever terrified Peter the way Venom did.
1) Knows his identity.
2) has all the same powers... only stronger.
3) can camoflage anywhere
4) Doesn't trigger spider-sense...
and
5) Wants to murder you and eat you....
Venom was a straight up Boogey man that Pete running terrified in flop houses hiding from him. Nobody else really hit that level of fear. Kraven, Osborn, Carnage... theres a lot of Hate and anger there... they may cause more damage than Venom would... but that single minded pursuit was something kind of new. Venom didn't want to rule the world, or take over the mob or destroy the city.... he JUST wanted to KILL Spider-man. Nothing in his life would take priority... it was like a terminator robot.
At least back then.
Now days? I think Morlun tried to fill that role, but wasn't done as good. He may feel responsible for Carnage.. but i'm not sure he's really 'scared' of him.
I remember in Venom First Host the last mini-series before Donny Cates run by Mike Costa, Eddie invited Harry for a beer and Harry actually accepted and they reminisce there time as Spider-man enemy and their pursuit, Harry didn't look at his time as the Goblin very fondly with no pride whatsover but Eddie took satisfaction that Spidey was more afraid of him than the Goblin. I thought that was a cool scene.
I do not think he is scared of Doom. One thing about Peter is he understands how to handle people, and the best way to handle Doom is to speak to him straight up. I also do not believe Victor is superior in every way. He has a flaw, and it is his ego ( very much like Otto). That knowledge is something that helps Peter when dealing with Victor. One person I know he is scared of is Hulk. He knows he cannot beat him physically, outsmart him, or reason with him.
He is probably scared of Venom due to the fact Venom stalked him before and the symbiote not triggering his spider-sense. I would also say Morlun, although Morlun hasn't been a recurring villain.
I think he is scared of what the Green Goblin can do to his loved ones more than he is scared of Norman himself.
I remember reading ASM 350 and I was a huge Spider-Man Fan back in those days. Doom mopped up the floor with him but I had zero problems with the way that issue was handled. Doom is about as bad as it gets. Spider-Man got an ultimatum and did his best to resolve the problem. It still ranks today as one of my all time favorite issues.
Most cases I like it when the hero is faced with an opponent where force vs force isn't going to do it.
That was always one of all time favorite fights.
Honestly, for Doom being a top grade #1 baddie in the marvel universe... i rarely see him written that way. He talks big, but when push comes to shove he always comes up short. NOT that time. He beat Spidey so hard he was able to have a heart to heart talk with Uncle Ben!
That was a Doom that was competant and powerful and worthy of all the years of grandstanding he's done. And yeah,... Spidey knew he couldn't take him at that time.