Rocky Horror Picture Show springs to mind. First saw it as a young teenager and thought "what the heck is this thing?!" But a few more viewings and I came to love the movie.
I can only think of one example, and that's 'Monty Python's and the Holy Grail'. I was completely bored with the movie the first time it was introduced to me, and couldn't fathom what anyone saw in it.
As the follow up to Pulp Fiction, I hated this movie first time I saw it. Years later, viewing it again I really appreciated what a well crafted movie it was, just not in the same vein as PF. I still like Pulp better (and several other ones) but Jackie Brown is a great movie.Jackie Brown. I guess I was expecting something more like Pulp Fiction the first time I saw it, which means I was clearly expecting the wrong thing. Now I consider it easily among the best Quentin Tarantino has done, and rank it higher than Pulp Fiction.
Conan the Barbarian. It was so devoid of dialogue that I thought it was kind of boring. Then I learned more about the soundtrack and how it was intended to carry much more of the drama. It made a lot more sense after I knew that.
Aliens. Scared the crap out of me but I was 8 or so. Didn't finish it and went to bed early.