The Grapes of Wrath (1940), from John Steinbeck's Pulitzer-winning novel, and a story that got them all branded 'Commies' by the McCarthy-run HUAC; it's simply a humane story about every person deserving some dignity, justice, and work in life.
Next I prefer his best western, The Searchers (though She Wore a Yellow Ribbon is also a great one in spite of the title), then non-westerns missing from the top 1000, The Informer (1935, about IRA terrorists, for which Ford favorite Victor McLaglen won his only acting Oscar), and Mister Roberts (1955, a comedy about a naval supply ship during WW2, he shared directing credit with Mervyn Leroy). It’s good to see the underrated My Darling Clementine rising over time, it’s the one about the gunfight at the O.K. corral, with Wyatt Earp, Doc Holliday, and the Clancy Brothers; it may be Ford's finest b&w western.
They Were Expendable (1945) is also an underrated war film, about the PT boats and their crews. It was his first film after making war propaganda films for the government’s war effort from 1941-1945, and he used that experience to make a taut, realistic and often overlooked war film about a little known part of the Pacific war, that of the U.S. patrol boats, which were mobile but small and vulnerable, hence the title.
1. Searchers, The (1956) #65
2. Man Who Shot Liberty Valance, The (1962) #107
3. Grapes of Wrath, The (1940) #144
4. Stagecoach (1939) #283
5. My Darling Clementine (1946) #315
6. Quiet Man, The (1952) #425
7. How Green Was My Valley (1941) #528
8. She Wore a Yellow Ribbon (1949) #765
9. They Were Expendable (1945) #782
10. Young Mr. Lincoln (1939) #865
The other cavalry film, Fort Apache, should also be on this list - it's ranked 1998th this time. I'm always bored by Stagecoach, The Quiet Man, and How Green Was My Valley, but they're still all finely crafted - but "that's just my opinion, I could be wrong" (Dennis Miller).
As always: your results may vary, void where prohibited, not responsible for accidents
See the full list of top ranked 100 directors here: Top Ranked 100 Directors, 2011 Edition