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.
Acceptable Targets: After Max's air-conditioning unit falls out of his appartment and crushes a mime artist.
Narrator: "Luckily, [Max's] manslaughter charges were dismissed, because he was labeled mentally deficient, and unlikely to have a motive for killing a mime artist. Unlike most people."
Alternative Character Interpretation: A minor one, as people debate whether Max was more upset about Mary using him as a "case study" without his consent, or whether it was her expressed desire to cure his Asperger's.
Nightmare Fuel: The "Que Sera Sera" sequence, especially when it shows that Mary is with child.
And when Mary finally visits Max, and cuddles up next to his corpse.
Vera accidentally drinking formaldehyde after mistaking it for sherry. Made worse by the slow, chantingLeitmotif and the fact that similar incident have happened in Real Life.
Screwed by the Network: In the US, IFC chose to release it straight to DVD instead of giving it a theatrical release like other countries. As a result, the film was ineligible for Oscar nominations (a Best Animated Feature nomination was expected had it gone to theaters).
Tear Jerker: Again, the "Que Sera Sera" sequence, and all that built up to it. Mary's sheer misery and self-loathing is utterly tragic.
Mary's second letter to Max as a child, in which she details a bully grabbing her sandwich and pissing on it, then making fun of her birthmark. This culminates in her crying as she writes the letter, even telling Max her tears are smudging the paper, then asking him as her voice is breaking if he's ever been bullied.
Max: You are my best friend. You are my only friend.
Ugly Cute: Mary. Well, maybe not ugly but given the style of animation, as well as her whole character, it sort of fits.
What an Idiot: When Max writes to Mary and tells her of his AS diagnosis, he makes it clear that he doesn't like the idea of being cured, as he does not see anything wrong with having AS (a sentiment held by many real life people with AS). Yet, when she writes him after graduating college, she apparently expects that he will be pleased by the news that she is researching a cure and hopes to celebrate this fact with him.