Don't tell us you're surprised, folks—after all, memories literally are the whole movie. Eternal Sunshine of the Spotless Mind takes place within the memories of Joel; it's a movie that explores how and why we remember things—and the impact that these memories have on our lives. It's also about what happens when these memories disappear: does the self created by these memories also go away?
Joel's firsthand experience with his own past gives him personal insight into who he is and what he and Clementine had together when things were going well. But over the course of the movie, even his memories of memories are washed away, and he becomes like a blank slate, ready to move out in the world and relive the last two years of his life.
The flaw of Lacuna's process is that the memories must be erased. If Lacuna could simply remind people what their past experiences were like without getting rid of them, their treatment would lead to happier, healthier individuals.
The only reason Joel decides he wants to save his memories of Clem is that he has forgotten all the bad memories already.
Memory and identity are inseparable. Our accumulated experiences are how we form a conception of what it means to be us. If you suddenly forgot everything you've done, you won't know who you are. What if you start thinking you're a high-school student when you're really a rocket scientist turned astronaut, or fifty-three aliens simulating a human life-form? Hey, it's unlikely, but you would never know.
In Eternal Sunshine of the Spotless Mind, Clem and Joel both have their memories wiped so that they can forget each other. Their memories of the last two years centered on each other, and now, with their memories wiped, they feel lost and empty. It's not a surprise, because they have both lost pieces of themselves in the erasure process.
You can never really change who someone is. Even though Clem and Joel have had some memories erased, they're still the same people they used to be, minus a few kisses and arguments.
Joel and Clem can never have the relationship they first had, because their identities have been altered by the information that they were once together. This will always be with them, affecting the decisions they make and ultimately affecting who they are as individuals.
Everyone wants to be happy. In fact, maybe that's the only thing that anybody wants. But happiness can be hard to come by, especially when you're trying really hard to be happy instead of just enjoying what you have. This is what seems to be happening to Joel in Eternal Sunshine of the Spotless Mind: he's discontent with who he is and the funk he's stuck in. He can't make eye contact with a woman he doesn't know, and apparently his relationship with Naomi is a little rocky.
So when Joel meets Clem, he thinks she's going to be the one to pull him out of his rut and make him feel alive. The problem is that he doesn't listen to her when she tells him that's exactly what she isn't going to do; she's just another person looking for happiness, too, like Patrick and Mary and all the other characters in the movie. Unfortunately, Joel finds out that when true happiness finally comes, it can be fleeting.
Eternal Sunshine shows that it's wrong to make another person responsible for your happiness. Joy and fulfillment should come from within, not from some exterior source whose constancy is unreliable.
Being happy is all about surrounding yourself with happy people. Only when Clem and Joel grow apart do they become unhappy. Sharing happiness is a necessity.
Just because Eternal Sunshine of the Spotless Mind isn't a horror movie, that doesn't mean it isn't scary. Joel is forced to deal with some difficult things inside of his own mind, but it's not just in his memories that Joel is afraid. He's also afraid when he meets Clem again; he's afraid to make eye contact, afraid to start a relationship, and just as afraid to give up the past. But that's kind of the point, really: relationships are scary. Life is scary. None of it is easy. But will running away and erasing everything painful make it any better?
If Joel weren't so afraid, he never would have had the Lacuna procedure done. Fear makes him an escapist.
Joel's fears of intimacy are only seen post-procedure and are actually a product of the emotional trauma he experienced from losing Clem. Even though he can't remember it, the emotional core of the memory still exists.