Preminger’s Anatomy of a Murder pushed the envelope back in 1959. Not just concerning rape, but all sorts of previously taboo topics.
Casualties of War
The Accused
Straw Dogs (original and remake)
Pulp Fiction
Rob Roy
I had to think for a minute to remember the rape in Pulp Fiction. 
For another bleak entry, there’s Martin, George Romero’s flick about a guy who thinks he’s a vampire and attacks women, injects them with tranquilizers, rapes them, kills them, and drinks their blood. It was made in the 70s and so is perfectly fine have no likeable characters or moments of joy or lightness.
Heaven’s Gate. Not totally a rape movie but has at the center one of the most disturbing rape scenes I have seen. Still resonates after all these years.
Sudden Impact
IIRC, Gone With The Wind had a spousal rape scene. Rhett carries a kicking Scarlett upstairs, the next day she’s happily combing her hair.
I could be wrong, though.
An uncensored for television cut of Flesh + Blood (Flesh+Blood (1985) - IMDb) starring Rutger Hauer and Jennifer Jason Leigh. It’s not as highly graphic as if could be, but it realistically shows what would have happened to a woman captured by a band of medieval mercenaries. There is however a big difference between some of the versions of this movie that get shown on regular television (where it comes across as a slightly rougher medieval romance) and what the original cut (in which they don’t hide the rapes and sexual abuse).
Hannie Caulder - The title character (Raquel Welch) is raped, and her husband murdered, so she learns to shoot and goes after the bad guys.
For a Few Dollars More - Col Mortimer (Lee Van Cleef) seeks revenge on the man who raped his sister.
The French movie Baise-moi opens with a graphic and disturbing rape scene of two women. One of the women then goes on a killing spree but it’s not clear if this was a result of the rape.
*The Fountainhead *contains a rape “by engraved invitation.” Dominique does everything short of yanking Roark by the balls and flinging herself under him on the bed.
Naked Vengeance. The sheriff was trying his darndest to look like Clint Eastwood. I must be gay to be thinking of that instead of the nude scenes.
Just opened up the IMDB site and found this list. Timely.
Let’s not forget GOLDFINGER – James Bond rapes Pussy Galore and she turns from the dark side.
The Pulp Fiction cite reminded me of Lawrence of Arabia (where it was basically implied).
John Boy was a bad boy in Last Summer.
A Time to Kill, maybe?
Well, she does get her new fireplace hearth out of it, too.
Speak with Kristen Stewart turning in a quite acceptable performance and Bastard Out of Carolina, wherein Jenna Malone is raped by her stepfather and I was ready to murder Jennifer Jason Leigh’s character for letting her daughter be treated so badly. Jenna Malone was awesome in this part, BTW.
The Wild Angels I found by accident while looking up some Easy Rider trivia. Peter Fonda and Bruce Dern are biker gang members. When Dern dies the gang rapes his wife in a crowded room during the wake, his real life wife Diane Ladd. A disturbing flick, to be sure.