The Spanish input - including any possible references to the spanish Civil war - is still unreclaimed territory, I would say. Still, we have been discussing it:
I remember A Bullet for Sandoval was based on a legend of Spanish bandoleros in Napoleontic times, and originally was set in those days too, they only decided to make a western (set on both sides of the Mexican-American border) of it for commercial reasons. If they had references in mind to more 'contemporary' events, I guess the Spanish Civil war is a more logical choice than the Mexican revolution.
I haven't seen Killer Kid, but the credit sequence of Run Man Run reminded me of Picasso's Guernica. If it's a reference it's a rather vague one, but I just got the idea when watching it;
Most Zapata westerns were directed by Italians (Damiani, Corbucci, Petroni) and I don't think they ever had the Spanish Civil war in mind. Mexico was seen as a third world country (and left-wing intelectuals like to identify with the Third World) and furthermore the Mexican Revolution served as a metaphor for the revolutionary ideas that were in the air during the sixties among intellectuals in Southern-European countries. The Spanish Civil war had attracted attention, and young left-wing intellectuals from other countries, but it had failed, Spain was ruled by a dictator now. Those left-wing intellectuals hoped for a better, socialist future (at least in the days before May '68). France, Italy and Germany formed the heart of left-wing Europe in those days, the most influential philosophers (some still living, some from a recent past) were Sartre, Merleau-Ponty, Marcuse, Bergson, Adorno. Spain was not of crucial importance to most intellectuals. Spanish artists of major importance, like Buñuel and Picasso, were working outside Spain.
Note: I'd like to repeat that I'm not an expert on Spain and its history. I only recently started to study the language (it's still some kind of imperfect Italian to me) and I hope to fill this gap in the future.