Through twists revealed by the end of the movies, Chinatown (1974)
, Angel Heart (1987)
and Lone Star (1996)
have incest as plot points, but I wouldn't say they "deal" with the issue (Lone Star
addresses it more than the other two).
In the final bit of The Grifters (1990)
, a desperate mother seduces her confused son in order to steal his money (though they don't actually "do" anything), and in The Manchurian Candidate (1962)
an incestual relationship between mother and son is certainly implied - though not addressed (it was the '60s after all). The House of Yes (1997)
is an off-beat dark comedy that has an incestual relationship between brother and sister. Natural Born Killers
has it as the backstory of the Juliette Lewis character, presented as a sitcom from Hell.
The Barbara Streisand flick Nuts
also has a plot twist that reveals incest, and there is an attempt to deal with it in a serious manner, though looking back as an adult and finally confronting her abusive father. A Thousand Acres (1997)
does this too.
The Color Purple (1985)
and The Dangerous Lives of Alter Boys (2002)
also feature incest. I think one of the patient's subplots in Girl, Interrupted (1999)
is ultimately about incest too.
A darkly comic coming-of-age flick that uses incest rather plainly is Spanking the Monkey (1994)
, where a son home from college caring for his mother, who is house-ridden due to a broken leg, starts a bizarre consentual relationship.
Those are all mainstream - or in the case of the few that are more recent independent films, films that garnered a lot of mainstream critical attention. As for which is the "best", I suppose that depends entirely in what you're looking for.