dave you should update this topic to correct, add, etc., to the list to get an up to date consensus, if you are up for it. 
I'm your huckleberry.
Here's where I think we are at this point, and we still aren't up to 30. I'm ignoring Frayling's nuttier ideas and sticking with what is more or less the consensus here. I'll be happy to consider suggestions to add.
Ace in the Hole (1952). The belt-and-suspenders remark comes from here.
The Comancheros (1961). The names McBain and Sweetwater come from this film, as does the image of a man drinking two-handed and slowly revealing that he is handcuffed.
Firecreek (1967). A ruthless Henry Fonda and his gang come to town to torment part-time lawman Jimmy Stewart and his fellow citizens. The town of Firecreek is compared unfavorably with a prosperous nearby community, Sweetwater. Fonda’s character is undoubtedly a prototype for Frank in OUATITW (SL may not have seen this film).
Fort Apache (1948). According to Sergio Leone: “The glacial Henry Fonda of Once Upon a Time is the legitimate son . . . of the intuition that John Ford brought to Fort Apache.”
Forty Guns (1957). A cinemascope Western, it employs several devices that would become SL staples, notably the ultra-close close-up of a character’s eyes. The film also ends with the title re-appearing; SL would later adopt and adapt this practice, making his audience wait for the conclusions of OUATITW and DYS to see those films christened.
High Noon (1952). Three baddies wait at a station for the noon train bringing Frank, similar to what happens at Cattle Corner at the beginning of OUATITW.
How the West Was Won (1962). There is an auction scene where Debbie Reynolds has to sell an expensive mansion for a song. The film concludes with Debbie Reynolds traveling in a four-wheel buggy through Monument valley with the Prescott family and a horse named Sam.
The Iron Horse (1924). The prototype for all railroad-building Westerns, inevitably referenced in OUATITW. The arrival of the locomotive, which travels over the top of the camera, is a direct quote. The shots of the rail gang at the end also seems inspired by the Ford picture.
Johnny Guitar (1954) Much of the plot for OUATITW comes from this picture, but there are also specific visual references. Vienna has a model of the railroad and the surrounding town; Johnny Guitar rides through railroad workers, much as Sam rides through railroad workers in OUATITW. And possibly Harmonica’s harmonica is a nod to Johnny Guitar’s guitar.
Jubal (1956). Not a reference as such, perhaps, but a reaction to an exchange that occurs between Ernest Borgnine and Glenn Ford.
--You know much about women?
--I can’t say I do. Why?
--Mae. Things ain’t right between us. You’ve been around. You’ve seen us. You know anything I can do to make her like me better? Of course, I can’t change this ugly face none but maybe some things I do, I don’t do right.
--There’s a lot of things a man does that bother a woman.
--Like what?
--Like slurping coffee out of a saucer.
--Yeah?
--Spitting. Scratching. Whacking her on the behind when she isn’t looking.
--Why, I always do that.
--You mean, in front of company?
--Why sure, if I just swat her in private—
--Do you think she likes being swatted?
--Don’t all women? Shows them you love them, don’t it?
--There are other ways, you know, Shep.
--Of course! Why, that’s exactly what’s been bothering her.
--That’s right. She’s just fed up with being whacked on the rump.
--Thanks for the tip, Jube.
It’s likely that SL used the following speech, from Cheyenne to Jill, as his response to the above: “You know what? If I was you I’d go down there and give those boys a drink. Can’t imagine how happy it makes a man to see a woman like you. Just to look at her. And if one of them should, uh, pat your behind, just make believe it’s nothing. They earned it.”
The Quiet Man (1952). The final flashback in OUATITW is shot and edited in such a way as to resemble the flashback of John Wayne killing a man in the ring.
The Last Sunset (1961). Kirk Douglas and Rock Hudson square off for a duel at the end that some feel was the model for the showdown between Harmonica and Frank.
Last Train From Gun Hill (1958): Anthony Quinn’s son does not approve of his father’s remarriage to an ex-dance-hall girl. In OUATITW, the oldest McBain boy similarly objects to his father’s remarriage.
Man of the West (1958) Julie London has her dance hall clothes ripped off her; perhaps this inspired the scene in OUATITW where Harmonica tears off part of Jill’s clothing.
The Man Who Shot Liberty Valance (1962). Lee Marvin, Lee Van Cleef, and Strother Martin terrorize town residents during a local election meeting, similar to the way Frank’s men act in the auction scene in OUATITW.
My Darling Clementine (1946). The climactic shoot out at the OK Corral unfolds with sound effects but no music, undoubtedly a precursor to the “silent” opening sequence in OUATITW. Menacing men in dusters appear here as well.
Night Passage (1957). Jimmy Stewart is The Man With the Accordion.
The Paleface (1922). Jack Elam’s duel with the fly in OUATITW is an homage to Buster Keaton’s butterfly problem in this film.
Pursued (1947). Frayling suggests the recurring flashback structure in OUATITW is copied from the one used here. Since SL had already used the device in FAFDM, however, it might be just as appropriate to say Leone is quoting himself.
Red River (1948). There is a moment in the film when Clift slides a lantern across a darkened room to dramatically reveal Joann Dru’s face, an effect later used by Leone—when Cheyenne first confronts Harmonica—in OUATITW.
Run of the Arrow (1957). Charles Bronson plays a mute Indian boy who communicates by playing his harmonica. This is a possible inspiration for the character Harmonica in OUATITW.
The Searchers (1956). Aaron Edwards sees suspicious signs in the desert surrounding his house just prior to the massacre (for example, the partridges fly away as if spooked). This is clearly referenced in OUATITW just prior to the McBain massacre. Also, the shot of Scar from the girl’s POV after the massacre is similar to the one Timmy has of Frank after his family is killed. Finally, it may be Ford's use of back-lit doors in this film that inspired SL to begin his own doors fixation.
Shane (1952). Joey Starrett mimes the stalking of a deer, rifle in hand. In OUATITW, Timmy McBain mimes shooting birds.
3:10 To Yuma (1957). Glenn Ford whistles the title theme to pass the time. The sequence in OUATITW where Fonda is stalked by his own men in the streets of Flagstone is appropriated and adapted from the climactic sequence in 3:10 where Ford’s men come to free him. And of course, in OUATITW, Keenan Wynn decides to send Cheyenne to a “modern jail” in Yuma.
Warlock (1959). Fonda kicks a crutch out from beneath a cripple who has annoyed him, similar to what he does to Morton in OUATITW.
