I watched it when I was in college, and now again in graduate school after I learned about Freud and psychoanalysis. At that time it did not struck me much, but this time it is mesmerizing. I saw a lot of psychoanalytic elements in it - the child's sense of defeat and fear for not having mother's love, the outward expression of social awkwardness that is rooted in Joel's early school experiences, Joel's obsession with a peak at a woman's crotch that developed at early age with the caregiver, Joel's happiness in the sink/water (probably made him feel protected in mother's womb?) and his fear to drown (the babysitter seemed to shower him in the sink and he was afraid to step on the ice in Boston?), and his struggles within his psyche about whether he should break away from her (which is rooted in their conflicts in real life). There are probably more, but I cannot recall now (or perhaps I don't want to - a Freudian loss of memory to prevent facing something myself).
In a bigger picture, it also reminds me of Weber and Durkheim a bit. Joel, like his name implies, is a man who internalized the institutional logic. He's very mannered, conservative, and living in a "correct" life style. Clementine, almost on the polar opposite, is impulsive, insecure, adventurous, and living in a "fucked-up life" as she deeply reflects about herself. The two seem to follow the principle of like for dissimilarity - a kind of social solidarity that glues people together. Yet they are also similar in a fundamental way: they are both lonely and outsiders of the larger and "normal" society.
Perhaps everyone of us is in between Joel and Clementine, struggling with a proper identity in the world, constantly wondering what meanings we want to create for ourselves. This movie, very much like Freud's work, can help us understand ourselves and then make peace with our souls. In this regard, this is truly humanitarian, in the deepest sense possible.