In Indiana Jones and the Kingdom of the Crystal Skull, Indy tells Mutt that he learned to speak Quechua from Pancho Villa's forces. I remember that he had an adventure with Pancho Villa in The Young Indiana Jones Chronicles. Is this a reference to this adventure? If so, which episode was it?
Yes, it most likely is a reference to the Young Indiana Jones Chronicles. The specific adventure with Pancho Villa was shown in the first episode, the pilot "Young Indiana Jones and the Curse of the Jackal". It was also recut as the 6th film, Spring Break Adventure.
Lucasfilms considers most things in canon, with the feature films being the highest canon, and the tv shows as a lower canon. Conflicts between the two are handled by the higher canon being right. This is called Indycron, similar to the old Lucasfilms canon structure for Star Wars (before Disney changed everything). So events in The Young Indiana Jones Chronicles are canon to Kingdom, unless the film said otherwise. In this case, it directly references the events.
The Young Indiana Jones Chronicles of course, was produced by George Lucas, and Harrison Ford was even in an episode. The Crystal Skulls were even going to be used by Lucas in the the Young Indiana Jones Chronicles before the show was canceled. One of the writers for Crystal Skull, Frank Darabont, also wrote for the tv show.
The old Indianajones.com website (produced and managed by LucasFilm) featured an extensive fictional biography of Indy. This article included a wealth of information taken directly from the Young Indiana Jones Chronicles, including this snippet:
In the years following Anna's death, Henry Jones became consumed by his research regarding the Holy Grail. This served to distance him from his young son. In 1916, during a visit to extended family in New Mexico, Indy escaped his father's reach. A trip across the Mexican border swept Indy up in the Mexican revolution, and Indy briefly rode with General Francisco Villa.
Since, according to LucasFilm the Young Indiana Jones Chronicles exist within the same canon universe as the films, there's absolutely no good reason to assume that the film shouldn't directly reference the pilot for the TV series; Young Indiana Jones and the Curse of the Jackal.
The series is also referenced in Indiana Jones and the Kingdom of the Crystal Skull, when Indy describes his adventures with Pancho Villa (chronicled in the first episode) to Mutt Williams.
The first episode of the series was Young Indiana Jones and the Curse of the Jackal:
Indiana finally caught up again with this jackal shaped artifact in 1916, after getting himself involved in the Mexican revolution while crossing the border with his cousin Frank. Having joined up with Pancho Villa, Indy became fast friends with Remy Baudouin, another revolutionary who originally hails from Belgium.