Clementine dyes her hair many vibrant, non-natural color. Each one could represent a specific stage of her and Joel's relationship.
Green: Upon their first meeting, Clementine has green hair. Green usually symbolizes newness and this would be the start of their relationship.
Red: Pretty obviously love. After their first initial meeting, Clementine and Joel are starting a new relationship and are falling in love.
Orange: This one is a little complicated, but it could symbolize a few things. One is fire. At this point in time, their relationship seemed to be peaking then going into a downward spiral. The "flames" of their romance is at its height (this is when we see a very intimate moment where Clementine tells Joel about her doll). Then we see where it starts dying down; it's still burning but they are both becoming unhappy with each other. Going with the fire idea, their relationship is end in a fairly destructive manner wreaking damage upon both of them. Another interpretation is that orange is not a primary color and it made of red and yellow. Their relationship has moved from the initial love struck phase into a more complicated level.
Blue: The very final color is blue, representing sadness. Clementine is clearly out of sorts and rather unhappy after they have broken up and had her memory removed.
At the beginning of the movie, we see Joel and Clementine meet for what we think is the first time. Later, it is revealed that he was taken there by a subconscious urge from Clementine's last message that she whispered to him before disappearing. However, this really is the first time they were meeting, and the memory he has of meeting her at a beach party is a ploy he made up to stop them from erasing his real memories of her. At the end, they listen to the tape together that Mary Svevo sent to all of the people who had their memories erased. This did happen in reality, but then Joel went back to the erasers to get his memories erased again, and that's what we're watching there.
- Alternatively, the erasing witnessed in the movie was a second erasing. The beginning of the new relationship with Clementine shown at the start and end of the film happened afterwards. Much like they were getting back together after the erasing shown, before the relationship that was erased, they were in a relationship that they erased. Evidence for this is the memory of the first time that they met in the erased memories. There are two things that come together to suggest this. First, the similarity of the meetings. Second, in the erased memory Joel says that Clementine approached him as though they had been lovers. For the meeting after the erase, we know this to be true. It could also likely be true for the erased memory.
- This is supported by the alternate ending, which reveals that Joel and Clementine have been meeting, breaking up, erasing their memories of each other and getting back together again for years and years.
It's pretty unlikley that the two of them just went back to having a normal relationship, especially supported by the WMG above this one. It may have been an alternate ending, but it's still a plausible thing that ties in with the actual film's future off-screen.
- I'm not sure which ending I watched, but I seemed to notice that the scene at the very end where they frolic into the horizon on the snow-covered beach is repeated a few times divided by several jump-cuts, while Beck's song is playing. This could be a hint that they are repeating themselves again and again and again.
Having their tapes and memorable items back, Joel and Clementine manage to retrieve some of their deleted memories, likely without or with a severely diminished "emotional core". This means that they can have a somewhat objective look at them and learn the lessons they were too emotional to draw from them before.