These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Base: Brian Cox' portrayal of Lecktor is weird to see for someone who has seen Hopkins' Lecter first, but while Hopkins has an Oscar to back his version, more and more people are starting to let Cox' Lecktor in from the cold as Manhunter achieves cult status.
Covered Up: This film, and specifically Brian Cox's take on the Hannibal "Lecktor" character, has been covered up by the later Thomas Harris adaptations and Anthony Hopkins' portrayal of Hannibal "Lecter".
Fridge Brilliance: You might find all of the stark colors strange, and attribute it to Michael Mann's The Eighties standard, but then you have to understand that the entire film is about perception and seeing ("Ever see blood in the full moonlight? It's quite black"), and Dollarhyde works as a photo developer. It's purposeful irony that his object of lust is blind.
Funny Moments: Falling asleep on an airplane with a folder full of crime scene photos on your tray? Bad idea.
Life Imitates Art: William Peterson found the role of Will Graham mentally exhausting and had trouble shaking Graham's characterisation even when he went on to other roles (he had to radically change his own appearance in order to look in the mirror and see someone else, according to The Other Wiki). Very appropriate, given that he's playing a criminal profiler who was institutionalised because he couldn't shake the thoughts of the serial killers he hunted.
Moment Of Awesome: Will Graham bursts through the window of Dolarhyde's house in slow-motion, set to "In-A-Gadda-Da-Vida".
The opening scene in which the killer goes to his victim's bedroom - seen through his video camera - just as the mother awakens, Freddy Lounds' fate, Lecktor's subtle lines ("Dream much?") and his phone call are all well and frightening, but Tom Noonan as the Tooth Fairy is pure Nightmare Fuel, especially when he captures Freddy Lounds.
Meta example: Tom Noonan didn't want to interact with any of the other actors unless they were filming, to make their reactions to his character's disturbing behavior more realistic. He even went as far as to sequester himself in his trailer between scenes, take different flights to filming locations than the rest of the crew, and staying in different hotels. The results speak for themselves.
Noonan has joked about this though and implied that some of the "steps" he took to this effect were not meant to be taken seriously- for instance, he was asked about the lighting in some of the scenes and replied "Francis doesn't like the light" as a bit of a gag, only to find out later that they really did turn the lights down and he ended up having to do all of his scenes in darkened rooms, because he was too embarrassed to correct them.
Nightmare Retardant: The revelation of what Hannibal's secret code to Dolarhyde is in the letter he sends happens shortly after the letter is published in the original book and 2002 film, and it's a very frightening moment. In Manhunter, it happens directly after the scariest scene in the movie, and in a ridiculously casual way (it's practically "Oh by the way, Will, Lecktor gave away your home address.")
Love It or Hate It: Other viewers find it quite an effective scene. It happens after the "scariest scene" because its meant to be an example of From Bad to Worse, and Crawford is not being casual but just being subdued and yet professional, giving the hidden message appropriate gravitas yet trying to assure Will that his family will be safe and there is no need to panic, possibly keeping in mind that if the Tooth Fairy keeps to his pattern they are in no immediate danger. One might even say the 2002 movie misses the point by making everyone freak out- it might make them more human, but it also makes them look less like the elite law enforcement agents they are supposed to be.
Three Scene Wonder: Lecktor appears in only three scenes, but he casts a pall over the entire film. Cox's take on him is a slimy, reptilian version, with cold, black eyes and a seemingly toothless mouth.