You're probably hear from others about all the popular ones like "Dead Calm" and "Captain Ron."
My favorite, however, is harder to find. It's "Knife in Water," (Nóż w wodzie) a 1962 film by Roman Polanski that was made in Poland. The story and characters are pretty intense, but it's also cool that most of it is set on an early folkboat, and it covers an overnight trip complete with below decks scenes in the evening. Simple, strong, graceful film.
For more info, see
http://www.imdb.com/title/tt0056291/
It's available on Netflix, but be warned that it's black and white and subtitled. However, I don't think I've seen a film that was so realistically set on a small yacht. In the additional DVD materials, Polanski talks about how he was doing a lot of sailing at the time in the area shown in the film.
Jim H