First of all, I don't want people to misinterpret this Take: I'm not advocating rape or any sex crime. They are abhorrent and cruel actions. Crime is a bad thing. Anal rape isn't the only way a man can be raped or sexually assaulted. These movies do a good job acknowledging the elephant in the room.
In this movie, the protagonist played by Denzel Washington is tied up on a chair and is raped by a woman. Before he is raped, he begs to not be raped. I can almost guarantee you that a lot of people thought it was funny, unfortunately.
"I'll Sleep When I Die" (2003)
In this movie a man (played by Jonathan Rhys Meyers) is walking in a street at night, and two men ambush him and drag him into a alley. As the two men restrain him, the male antagonist rapes him. The man commits suicide out of guilt for involuntary pleasure. It is not meant to be a comedy.
In Hell (2003)
A 21 year old man (Chris Moir) is in prison and is constantly raped by other prisoners, and eventually he succumbs to his injuries.
Bigfoot County (2012)
It's a found footage movie; towards the end of the movie the protagonists are kidnapped by a group of men that live in the woods. One of the protagonists is bound and gagged. The group of men ogle him and then hold him down while they rape him.
Messengers 2: The Scarecrow (2009)
A man walks into a woman's residence, the woman gives the man tea that has been laced with sedatives. After the man drinks it, he collapses and the woman proceeds to rape him while he is barely conscious.
The Rookie (1990)
Clint Eastwood's character is kidnapped and tied down and the female villain rapes him. As the female is squatting on him, she orders Clint's character to not loose his erection. Oh yeah, Clint directed this movie as well. Who would have thought that one of Clint Eastwood's characters would be in such a predicament? Clint did a good job directing this movie.
There are many more movies were these incidents happen but they are depicted in comedic ways which is why I didn't feature them here. For those who say The Game of Thrones has male rape scenes, only one of those parts is considered rape and I think it happens in the books not in the TV show. The Matrix has a scene where the male protagonist (Keanu Reeves) has his shirt ripped open and is pinned down on a table by two men and has a robotic bug placed on his stomach that burrows into his navel. It's not a rape scene but it's still not for the faint of heart. I've never been a victim of a sex crime and I don't want to be one. Rape happens to men in real life but a lot of men stay quiet about it due to shame.