I will not spoil the ending but I am going to spoil some of the plot points so if you think you can track down a copy and don't know the life story of Caravaggio and want to come to it a virgin, don't read any further than the pretty picture. (Note: all photos from the BFI book on Caravaggio by Leo Bersani; you can get it relatively cheaply at Powells Books.)
Caravaggio is told from the artist's deathbed in flashbacks. He's in exile after having done A Very Bad Thing, which is hardly a secret but I won't mention it here. The film deliberately draws attention to the fact that it's a reconstruction of history, not actual history; there are bicycles, trucks and typewriters in this Renaissance. I get a kick out of thinking of it as RPS (like Mrs. Brown or even Being John Malkovich -- it's all a matter of who's creating the fiction, isn't it?). The storytelling is slow and methodical; for instance, there's a long scene with a gymnast who's posing for the artist, showing off unnatural-natural body positions; that same character also has a monologue about perverted sex at aristocratic parties and later attends a party in the catacombs with rotting skeletons all around, the visual symbolism is quite heavy.
Anyway, what people want to know: Sean Bean plays Ranuccio, a fighter and part-time whore whom Caravaggio spots in a pub and invites to pose for one of his religious paintings that's giving him trouble. (The Church does not come off at all well; Caravaggio's sodomy and a friend's possible murder conviction are both ignored as long as the Pope and cardinals are happy with the work.) Michel -- short for Michelangelo, Caravaggio's first name -- and Ranuccio have a strange, twisted erotic relationship complicated by the fact that Ranuccio is in love with Lena, who ends up abandoning him for a nobleman so that her child (and presumably Ranuccio's) can be brought up wealthy. That kiss takes place right after Ranuccio stabs Michel in the side after a staged fight that Michel assumed was already over; he smears his blood over Ranuccio's face and says "Blood brothers," and Ranuccio kisses him. The blood-brothers idea comes up again later in an even creepier context.
There's not a great deal of physical contact between the two but there's a lot of smoldering gazes and uncomfortable looking-away when anyone else is watching. Lena accuses Ranuccio of being in love with Michel, which he denies -- says it's just for the money -- but even between Lena and Ranuccio, coins are used as erotic aids, so that's a loaded statement. My read on it is that Michel loves Ranuccio, which he says, but while Ranuccio isn't averse to sex with Michel, he loves Lena. And while Lena has a lot of affection for Michel and likes sex with Ranuccio, she's first and foremost a pragmatist; whoever has the most money will win her.
The core emotional relationship is between Caravaggio and his mute assistant, Jerusaleme, who is rather jealous of Ranuccio and wants to usurp his place in Michel's painting and his affections. He's not jealous of Lena despite the fact that Michel kisses her to make Ranuccio jealous. Actually, I can't decide whether he's only interested in Lena from an aesthetic point of view and as a way to Ranuccio or if he's genuinely attracted to her; he is devastated to lose her, but his grief seems detached, like mourning for the Madonna of his painting rather than someone he knew well.
The scene everyone here has probably seen screen-capped at The Compleat Sean Bean is where Michel gives Ranuccio coins to pose for him, and Ranuccio, who's accustomed to hiding stolen jewels and coins in his mouth, keeps putting them there until he's got a mouthful of gold and Michel comes up to him with one more coin between his lips to see if Ranuccio will take it from him with his own, which Ranuccio does. There's also a scene at the party in the catacombs where Caravaggio traps Ranuccio with his knife, upon which he has placed a ring that he ends up putting on Ranuccio's finger in a parody of a wedding.
I'm afraid to say more for fear of spoiling the entire movie...