i'm trying to think of ones that nobody thought of yet ...

horatio hornblower (the movie, someone already said the series!)
waterworld (yeah i know, but it has a sailboat in it)
lifeboat (alfred hitchcock, i got it at walmart on dvd)
the ghost and mrs. muir (ok, no boats, but a damn cool captain
and a fine movie besides)
the poseidon adventure
20 thousand leagues under the sea (hey that's sort of a boat haha)

that's all i can think of at the moment ...