Eddie Gaedel is famously the shortest player to ever appear in a Major League Baseball game. Who is the shortest player to ever appear in more than one game?

There are five MLB players listed at 5' 3", which is the shortest for anyone except Gaedel (who was 3' 7"). One of those players (Jess Cortazzo) also only appeared in one game, so he doesn't count, but the others, each of whom only played one season in the majors, are the following: (1) Pompeyo "Yo-Yo" Davalillo (1953 with the Washington Senators -- and his younger brother Vic was legitimately successful and played 17 years in the majors); (2) Ed "Stubby" Manger (1911 with the NY Highlanders (later Yankees)); (3) Robert "Bob" Emmerich (1923 with the Boston Braves); and (4) Michael "Mike" McCormack (1904 with the Brooklyn Superbas (later Dodgers)). [Some references also list Harry Chappas as 5' 3", but Chappas himself said that he was 5' 5" and the shorter height was listed only because of the record.] Because Davalillo was the most recent, with a brother who was a star, and he had his career cut short by injury instead of talent issues, he's often listed as the second-shortest (as Wikipedia claims), but there really isn't any way to know for sure. [BTW, Hall of Famer "Wee Willie" Keeler, who played 19 years in the majors, was 5' 4", so he was the shortest major star.]
From a Houston Chronicle article, which was quoted in the Yo-Yo Davalillo article in Wikipedia:

The shortest player on record is 43-inch Eddie Gaedel, who got one plate appearance (a walk) as a 1951 publicity stunt. Five players listed at 5-3 have graced the major leagues since 1900, according to Baseball Reference, with Pompeyo Antonio "Yo-Yo" Davalillo, Jess Cortazzo, Bob Emmerich, Stubby Magner and Mike McCormack combining for 90 hits in 463 at-bats.

https://blog.chron.com/ultimateastros/2011/08/18/astros-altuve-stands-shorter-than-all-active-mlb-players/
https://en.wikipedia.org/wiki/Yo-Yo_Davalillo
https://mightycaseybaseball.com/2020/02/18/happy-birthday-stubby-magner/

Here is a list of the 16 Shortest players in MLB history...

 1. Eddie Gaedel              --  3’7” 
 2. Stubby Magner             --  5’3” 
 3. Pompeyo “Yo-Yo” Davalillo --  5’3” 
 4. “Wee Willie” Keeler       --  5’4” 
 5. Freddie Patek             --  5'5" 
 6. Robert Maranville         --  5'5" 
 7. Bobby Shantz              --  5'6" 
 8. Lewis Robert "Hack" Wilson--  5'6" 
 9. Phil Rizzuto              --  5'6" 
10. Joes Sewell               --  5'6" 
11. "Sliding" Billy Hamilton  --  5'6" 
12. Jose Altuve               --  5'6" 
13. Joe Morgan                --  5'7" 
14. Mookie Betts              --  5'9" 
15. Dustin Pedroia            --  5'9" 
16. Ivan "Pudge" Rodriguez    --  5'9" 

https://www.themodestman.com/shortest-mlb-players-of-all-time/