Did Stan really not know about Mary and her interest in Howard? He just says he noticed one moment but never again, so it's unclear if he genuinely thought it was his imagination or he was just in denial.
How are Joel and Clementine going to cope with finding the truth out? The original script had a rather cynical ending where an older Clementine would go back to Lacuna intending to erase him - and being told that they have continued to do it over the years. That seems to suggest the two of them will learn nothing from their destructive relationship. However it's shown that Joel does his best to try and keep his memories from being erased when the procedure's actually happening. So perhaps they will give things another try and work on their relationship. Or simply they could decide that the whole ordeal isn't worth it and stay broken up.
While Clementine does have a lot of issues (notably being very impulsive), one has to wonder if Joel is overstating her bad qualities. The break-up is triggered by him saying she fucks people to get them to like her - which she herself later claims is false when they discover their memories have been erased. Perhaps the unhealthy part of the relationship isn't necessarily Clementine's wackiness, but Joel being too judgemental of her. He seems to look down on her, especially when he scoffs at the fact that she might want a baby. Notably when we're shown how they first met, Clementine in fact refused to be the other woman, saying that Joel had to split up with Naomi if he wanted to be with her.
Deleted scenes throw Howard's character into a whole new light. In the extended version of his subplot with Mary, he pressured her into having an abortion. This changes things from a mere workplace obsession on Mary's part to a full blown affair - Howard looking like he essentially Mind Raped her just to cover up his own mistakes.
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).
Although Kate Winslet would eventually win for The Reader, many still feel that this is the film she should have been recognised for. She was nominated but the only award she won for her performance was an Empire Award.
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.
Fanfic Fuel: It's become a source of fun for fans to guess how Lacuna's process would work in The New '10s with social media and smartphones to contend with.
"Funny Aneurysm" Moment: Mary's smoking pot and getting drunk in Joel's apartment is Played for Laughs. Not so much when Kirsten Dunst had to check herself into rehab for substance abuse and depression.
Harsher in Hindsight: In 2015, Jim Carrey's former girlfriend Cathriona White committed suicide with a drug overdose that included propranolol, a memory altering substance which several doctors have specifically likened to the procedure in the film. And a year later, her husband accused Carrey of providing the drugs himself.
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.
Paranoia Fuel: Patrick's behaviour causes some. When getting the procedure done, you invite these Lacuna technicians into your house for the evening and you're unconscious the whole time. They could do absolutely anything or take anything. And if something goes missing from your belongings, you won't know because in your mind they were never here.
Rewatch Bonus: The first portion of the movie makes a lot more sense after watching the movie a first time.
Visual Effectsof Awesome: Throughout the movie, greatly adding to the surreal, dream-like depiction of memories. Perhaps most notably, in a blink and you'll miss it moment during the memory of Joel and Clementine's final fight, Clementine is storming off on one leg.
The Woobie: Mary once her backstory is revealed. She had her memories erased of an affair with Howard, and it's implied he pressured her into it. According to the deleted scenes, she got pregnant with his baby and aborted it.