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.
Alternative Character Interpretation: Did Mark Ruffalo's character know about Mary and Howard's affair, or not? It's left ambiguous as he implies he only noticed something different about her personality when she was with him. If he's telling the truth, he's just unlucky that his girlfriend can't be with him as she has to work through her own issues. If he's lying and he did figure out what was going on, he's creepy and manipulative.
I don't see how this would make him 'creepy and manipulative'. Whenever the subject was hinted at he would get visibly withdrawn, his voice would go flat, etc. If he's lying, it could just mean things had screwed up once before and he just wanted a fresh start. Then it starts to repeat itself and he knows there's nothing he can really do about it.
Also failed to get nominations for Best Picture or Best Director for Michel Gondry (though the latter would share a screenplay win with Charlie Kaufman).
Crowning Music of Awesome: Beck's cover of "Everybody's Got to Learn Sometime", which plays over the ending as Joel and Clem chase each other in the snow.
The Polyphonic Spree's "Light And Day/Reach For the Sun," which has an Uncanny Valley-heavy music video on the DVD, and is featured in many supplementary documentaries and trailers.
Fridge Brilliance: Clementine's reasons for breaking up with Joel are how he never opened up to her. In trying to keep the memory of her he puts her in all the dark places he never let her into.
Also, of course Joel wants to keep his memories of Clementine, the procedure erases the most recent memories first. As the movie goes on, Joel probably forgets that he broke up with Clementine at all.
Not likely. In the last memory that's erased, the one where they first met, Joel acknowledges that he grew to hate her orange sweatshirt.
Joel doesn't remember "Oh My Darling Clementine" because, when trying to save her, Clem was in a memory of Joel's mom singing the song. Clem got erased from that memory, which by extension erased the song.
Fridge Horror: When Joel initially meets Clementine, he is well aware of the song frequently associated with her name. As a result of the procedure, he has no memory of it, despite its memory only be associated, not originated, with her. If details as insignificant as songs are being lost because of the mind wipe, what else were people losing? There are also a vast myriad of ways this procedure could be used in incredibly unethical ways - implied by Howard's pressuring Mary into having it done after their affair.
A little one concerning the song: it is stated that Joel's favorite toy during his childhood was a Huckleberry Hound doll. Maybe not horror, but having the memory of your favorite thing as a kid is still sad when you think about it.
When Joel goes to get his memories erased, look at the things the other patients are holding (the relics of people they're trying to forget).
After Joel's memory erasure is completed, Lacuna still have absolutely no idea that he tried to resist the procedure. One wonders how many of their clients realized they didn't want to go through with the procedure halfway through but were, like Joel, unable to stop it. Granted, the Lacuna employees react with surprise when Joel goes "off-map" and tries hiding in older memories, but perhaps it had simply never occurred to any of the other unwilling clients to try that.
From the deleted scenes, Howard pressuring Mary into getting an abortion during their affair explains why his wife's reaction to the resurgence of Mary's affections after the wipe was "Don't be a monster. Tell the girl."
Some of the mental images are disturbing - like the guy who literally has no front in Joel's memories, or the instance where Joel temporarily retreats into an "erased" memory. Not to mention scenes where reality apparently decays around Joel as the memory is erased.
Hell, just the idea that an essential part of your memories can be erased in your sleep. And you get to watch it happen.
Rewatch Bonus: The first portion of the movie makes a lot more sense after watching the movie a first time.
Tear Jerker: The scene under the covers when Clem talks about her "ugly" doll and Joel begging "let me keep this one."
Clem and Joel's first meeting and Joel's last goodbye to her memory.
Joel changing his mind about having the procedure after reliving a particularly fond memory of Clementine, and helplessly pleading for it to stop.