Princess Mononoke features violent conflict between two opposing factions, but neither faction is “bad” and both leaders are motivated chiefly by compassion for others.
Grease? You could make the argument that Leo (leader of the Scorpions) is a bad guy, but he’s pretty tame. Rizzo was just kind of a bitch, the way she revealed that Sandy stayed in the U.S.
Those are just normal teenager bullshit. I don’t think there’s an actual bad guy in the movie.
Being There
Groundhog Day
Might be controversial, but I’d argue for Ex Machina.
Caleb - a rube, but not a bad guy.
Nathan - a genius with a manipulative streak. But it was needed for his experiment
Ava - a trapped being trying to attain freedom.
The genius of the movie centers on which you sympathize with determines which character is the protagonist. Is Nathan holding Ava to protect mankind or is he imprisoning a sentient being? Is Ava the impending doom of the world or just trying to control her own life? Is she aware? Does she have natural rights? There’s a lot to unpack there.
Well, Caleb’s a dupe no matter what. I think we can agree on that.
Many movies with a “man vs nature” conflict would fall into this category. The Perfect Storm. Tornado.
And not fitting that category but just popped into my head: Searching for Bobby Fisher
The Great Escape
Well, except for The Nazis. 
The aliens with their incredibly destructive whale communications probe were definitely bad guys. At best, they showed complete disregard for the dominant intelligent species on the planet and nearly accidentally killed everyone, at worst genocidal maniacs who nearly deliberately killed everyone.
Phil might be the “bad guy”. Or maybe Ned. 
(especially if he is the true driving force behind Phil being locked into the cycle. And all simply in order to sell insurance policies!)
Local Hero.
4 Weddings and A Funeral (Andy McDowell’s Scottish Husband is a dick, but not a bad guy.
While You Were Sleeping.
Meh.
Since the probe was never really explained, it might as well have been a “force of nature.”
It wasn’t anthropomorphized at all.
And even if there were some minor “bad” people in the movie, they were not essential to the plot.
True enough, though the Russian whalers are the last in a series of obstacles in the crew’s quest to secure the humpback macguffins (which is the main plot). The Klingon ambassador is an antagonist for Kirk, in particular, but serves mostly to tie the film’s beginning back to The Search for Spock.
What about that monk dude? He seemed pretty much a bad guy - he wants the cash the forest god’s head would bring him, and doesn’t give a damn who gets killed so he can get it.
Yeah, the two main factions in Mononoke are both compassionate, but the profit-guy wasn’t.
And didn’t Twister have a rival team of storm-chasers who were stealing the protagonists’ technology? They weren’t as dangerous as the tornadoes themselves, maybe, but they were still bad.
The thread title is “Movies with no bad guys.” The op asks for “movies with nothing but good guys.” They are not the same thing. Although it seems like most American movies feature characters who are abstractions of good and evil, many Euro and Asian movies deal with characters equally capable of good or evil acts. Such characters would satisfy the “no bad guys” criteria, but not the “nothing but good guys” one.
King Kong (1933) - The ape is clearly meant to be taken as a tragic figure, not a bad simian. The tribe sacrifices young women to appease Kong, but hey, they’re just primitives trying to keep an existential threat from trashing their asses (and don’t forget the tribe comes to the aid of our heroes when Kong comes a-knockin’). The closest thing to a “bad guy” in the film is Denham, but he is just an over-enthusiastic filmmaker, not in any way malicious.
Sunset Blvd. (1950) - Norma Desmond is a tragic figure. Joe Gillis is a sleaze. They are both victims of Hollywood (and each other), but not bad guys.
I’m going to nominate Brigsby Bear. Technically a fail, since two characters are guilty of kidnapping a child and raising him in a bunker. So, obviously bad guys. But I think the film works with the spirit of the question. It is mostly about the kid’s attempt to create a movie after he is rescued. There are no traditional bad guys thwarting that process. Everyone in the community is supportive or at the very least has his best interests at heart.
Check out the No Antagonist listing at TV Tropes.
Frank is a bad guy, though. He looks at that young kid and says something like, “You’re too late. Great, you killed him.” The shocked/devastated look on that kid’s face solidifies that Frank is really bad.
I get what you mean, but Frank is worst in the movie than in the show. I don’t remember anything like that moment in the show.
Found the exchange:
**Frank Burns : You idiot, I said a cardiac needle!
Pvt. Lorenzo Boone : Do you want me to get a nurse?
Frank Burns : Too late, Boone, you killed him.
[Walks away; Boone starts to cry] **
Inside Out
Her parents cause some of the stress, but they aren’t “bad guys.” The conflict comes from the clashing of essential – but divergent – aspects of her personality.
Sticking just to Oscar winning movies…
Shakespeare in Love
Driving Miss Daisy
Rain Man
Out of Africa
Terms of Endearment
Chariots of Fire
My Fair Lady
Gigi
Marty
Going My Way