1) True Grit
2) The Searchers
3) The Man Who Shot Liberty Valance
IMHO, if your list of "Favorite JW movies" doesn't include The Searchers in your top 3, you simply don't get what the 50's-60's Western-movie-genre was all about.
There are 2 kinds of westerns (my favorites), John Wayne movies and all the rest. I also like a lot of his war movies. My order of favorites changes all the time.
Westerns
1. McLintock
2. The Cowboys
3. Red River
4. True Grit
5. El Dorado
6. Stagecoach
7. The Searchers
8. The Shootist
9. Big Jake
10. Rooster Cogburn
War Movies including US Cavalry
1. Rio Grande
2. Fort Apache
3. She Wore a Yellow Ribbon
4. Sands of Iwo Jima
5. The Horse Soldiers
6. The Longest Day
7. In Harm's Way
8. They Were Expendable
9. Operation Pacific
10. The Green Berets
Best of the other Genres
1. The Quiet Man
2. Islands in the Sky
3. Hatari
4. The Legend of the Lost
5. Hellfighters
6. Donovan's Reef
The Searchers
The Quiet Man
Red River
Rio Grande
Big Jake
The Shootist
In Harm's Way
Stagecoach
El Dorado
She Wore a Yellow Ribbon
The Cowboys
Rooster Cogburn
Hatari
The Man Who Shot Liberty Valance
Fort Apache
The Sands of Iwo Jima
Donovan's Reef
McClintock
Islands in the Sky
The Green Berets
Interesting that this should come up right now as there are two John Wayne movies on at this moment: AMC has "The Hellfighters" and TCM has "The High and Mighty" which was the movie "Airplane" was spoofed on.
Everyone of his Westerns. Did not care to much for his non-western films.
My father n law is a huge JW fan. He has every JW western made (well maybe not all but has alot). We spent a whole weekend a few years back and watched every movie he had. Good times.