Santa Cecilia (St. Cecilia) is the patron saint of music, which is an obvious reference to the Mariachi theme. Both Henry Purcell and George Frideric Handel wrote Odes to St. Cecilia's Day (22 November 1683, and 1739, respectively). Few hard facts are known about St. Cecilia who may not have existed at all, other than in legend.
The bar in the beginning of the film where Steve Buscemi and Cheech Marin talk is an actual bar in Acuna, Mexico called the Corona Club. The bar is a lot cleaner and bigger in reality, but it's like walking right into the movie. They also have quite a few pictures of the stars and crew of the movie on the walls.
The bathroom scene before the 2nd bar shootout was directed by Antonio Banderas. Robert Rodriguez said he didn't like using 2nd unit crews and Banderas asked if he could direct the scene, so Rodriguez agreed.
The movie was originally entitled "El Pistolero" ("The Gunman") to be consistant with the first film (El mariachi) but was changed at the request of the studio. In Mexico it was released as "Pistolero".
Robert Rodriguez had originally written a rock version of the song "MalagueƱa Salerosa" into the screenplay. It would later be performed by his band "Chingon" during the end credits of Kill Bill: Vol. 2.
Though Quentin Tarantino wasn't initially cast in the movie, the character he plays was based on him. Steve Buscemi was originally cast in the role, but when Tarantino expressed an interest he was immediately given the part.
During the shoot out in the bar Cheech Marin's character is rarely seen. This is because they could only shoot his scenes in the six days they had him, so they made an approximation of what the shot up bar would look like and shot his scenes with it, putting his character behind it for most of the shootout.
For most of the killings they used a gun that essentially fired fake blood at the characters instead of squibs. This unfortunately created too realistic of an effect resulting in them having to edit out much of the deaths for the censors.
The trivia items below may give away important plot points.
Late in the film we discover Bucho's real name to be "Cesar". Bucho calls El Mariachi "Manito". Manito is short for "Hermanito" in Spanish, which means little brother.