Jules' final speech sums up the movie perfectly: "I'm trying real hard to be the shepherd." The movie's theme across all stories is about bad people and criminals trying to do the right thing.
When Butch, having escaped from some rapists, decides to go back and save Marcellus from them. Even though Marcellus is a mob boss who was out to kill him less than a hour ago (and nothing guarantees that he won't keep trying to do the same afterwards).
Marcellus's reaction to the rescue has a subtle example: when Butch asks, "Now what?" Marcellus goes into a rant about the agony that awaits the rapists. When Butch clarifies that he meant between the two of them, Marcellus takes a second to remember that they had been trying to kill each other prior to the rapists interfering and promptly tells Butch that they are even (so long as they never see each other again).
Butch isn't a hero; he barely even counts as an Anti-Hero. He's a violent, brutal thug. But he does have a conscience and when he loses his temper he's ashamed of not being able to control his impulses. Just because he is abusive to Fabienne that doesn't mean he doesn't care.
Being high as a kite and overdosing unpleasantness aside, the outing between Vincent and Mia is quite sweet. Vincent, scared of the idea of being out with her after hearing what happened to Tony Rocky Horror, is adamant to Jules he's going to be indifferent to Mia, but is charmed by her over the course of dinner. There's a sense of tenderness when their crazy night is over and he holds her hand in agreement never to share the events with Marcellus, then blows a kiss to her departing figure.
There's even a tag in Butch's story: when Marcellus goes off to talk, Vincent hangs back to make sure Mia's doing okay and she thanks him for saving her life.
Yolanda's panicking when Jules holds Ringo at gunpoint makes you realize just how much she cares about him. And when Jules allows them to leave peacefully, they both leave clutching each other like they're about to burst into tears.
And it seems Ringo cares just as much, as when they leave the diner, he's got his arm around her shoulders and is clearly trying to comfort her.
Although it's Played for Laughs, the fact that Jules and The Wolf actually really seem to care about cleaning up the mess before Bonnie gets home, and therefore saving Jimmie's marriage, is really quite sweet.
Jimmie himself is more concerned with losing the woman he loves than going to jail for aiding criminals in hiding/removing evidence.
While The Wolf is abrupt and curt with Jules and Vincent (especially Vincent), he is unfailingly patient and polite with Jimmie, knowing he is an unwitting part of the situation and sympathizing with him.
Jules' Heel Realization: "But I'm trying, Ringo. I'm trying real hard to be the shepherd." And he lets Yolanda and Ringo go.
Not only does he let them go, he ensures that they leave with enough money to potentially establish normal, non-criminal lives.