Gus Van Sant is probably one of my favorite filmmakers, and this might be my favorite of his. Hard to say, he has a lot of movies I love for very different reasons. Maybe this isn't his best, but it's the one that most stirs up something inside me... I find something profound and moving about this film, but it's not quite describable. Some of it is in the fragileness and honesty of River Phoenix's performance... if Gus Van Sant's films are almost always about outsiders, then Phoenix is the most realized, most poignant one. Some of it is the visual aesthetic and tone of the film... quirky yet beautiful, show-offy yet soulful. Van Sant sort of did that "goofy, quirky characters with depressing lives" thing before it became more popular.
Mostly I think it's the sense of longing at the center of the film. Anybody who has ever felt like an outsider in their life can relate to that feeling of needing acceptance, if not by the society that you're in, then by someone that you care about. This is one of my favorite tales of unrequited love. Phoenix's character spends the whole movie trying to get the love of two people, his friend Scott and his long lost mother. He succeeds at neither, but there's is a tiny sliver of hope still at the end of the movie... or at least, it's not definitively a sad ending.