In the past few months, I've seen three films with exposed male genitalia. I doubt I will be giving any spoilers to say that Observe & Report, The Hangover, and Brüno all show the penis. They are all shown with the purpose of laughter, but only once did I laugh, and not coincidentally it was with the movie I enjoyed the most.
Observe & Report (2/5 stars) was funny enough, but it suffered from a moronic script, flat characters and stupid gags. The Hangover (4/5 stars) was not only funny, but it had a reasonable plot. I mean, I know these films are all fantastic, but at least make it mildly believable with characters that have a little personality. Finally, there was Brüno (3/5 stars), which made Borat seem cohesive. Brüno had many good sketches that just did not fit well together as a film.
It did get me thinking about nudity in film, either to titillate, to cause chortles or to enhance the art. Breasts are a dime a dozen. You practically get those in children's movies. Asses are also common, of both genders, men slightly less so. The penis is rarely shown in artistic contexts, and is almost exclusively used to shock and guffaw.
It is common to think that vaginae make a number of appearances in film, but that is confusing public exposure with pubic exposure. As Dimitrios Otis wrote, we often see pubic hair during "full frontal" scenes, but rarely do we see the vaginal lips outside of porn.
I can really only think of one film that had both vagina and penis used in a serious context is The Dreamers, the 2003 film from Bernardo Bertolucci. Bertolucci mixed his love of film with filming of love to show the lives of three youths in Paris during the 1960s, obsessed with cinema and sexuality. It's a curious film, but worth watching, especially because Eva Green holds nothing back. There are no secrets on my DVD.