Asshole Victim: Agent Sands kills a chef, just because he believes the guy made his favorite dish of slow roasted pulled pork too perfectly - and then justifies it as "maintaining balance." He also sabotages a bullfight by rigging the bullfighter's suit with an electric charge that paralyses the man long enough for him to be gored to death, so that he could profit off of betting on the bull. Sands later has his eyes removed, and is left alive to stumble around for the rest of the movie with blood coming out of his eye sockets.
Blown Across the Room: Oddly enough, it seems that the victim flies farther if he is shot with a smaller gun. Rifles and carbines cause people to crumple to the floor. El's shotgun sends men tumbling ass over kettle. And at one point, a wounded soldier is shot by what appears to be a holdout pistol and is literally sent sliding across the room.
Played with in that El shoots a guy who is falling down off a balcony, so this shot only accelerates him faster to the ground, and his death.
Body Double: Played With. They find a man who generally resembles Barillo. Then they cut off his face and kill him to make it look like Barillo had died getting plastic surgery. Ramirez figures it out when he notices that Barillo's jewelry was poorly fitting on the body's fingers.
Briefcase Full of Money: Subverted: Through most of the movie, there is never enough money to changing hands to fill a briefcase, so Sands puts it in lunch boxes. Which the money obviously still doesn't fill. By the end of the movie, the Mariachis end up making off with a sum of money so large, it fills both of their guitar cases and still leaves enough for them to end up stuffing their shirts with it.
Bunny-Ears Lawyer: Sands is a visibly eccentric character and uses often a pair of fake arms, which eventually turn out to be useful. He uses them to shoot an informant under the table and one last time to kill Ajedrez.
Captain's Log: Ramirez was constantly giving a running commentary on what he was doing into a concealed tape recorder, presumably to be used as a record of what he thinks is a semi-legitimate investigation into a drug lord.
If one assumes that he is the Hero of Another Story (as he is presented in the movie), then this could very well be the source of the narration if he were the star. As it is, he ends up spending much of the movie talking to himself and commenting on whatever foolish thing he is about to do, as well as justifying the fact that he is explaining (to nobody in particular other than the audience watching the movie) the significance of various minor details.
Marin's character has a reason: he thinks asking for a moderate payoff for his information would keep Sands from killing him. We don't know if Marin was right, as Sands kills him anyway for unrelated reasons.
Covers Always Lie - See the above picture with Salma Hayek in it? She's not really a major character because she's DEAD in this film and only shows up in flashbacks. Johnny Depp's Character is also of secondary importance to Antonio Banderas's, yet Depp is in the foreground.
Eagleland: Sands is a CIA agent manipulating Mexico by tricking a power-mad general, a drug overlord, political handlers, local drug agents, a retired FBI agent, and the mythic El Mariachi into playing against each other to "maintain the balance".
Even Evil Has Standards: There is one ridiculous scene in this movie where during a shootout in a church, everyone pauses for a few moments because an old lady who is the only person there besides the shooters all of a sudden gets up and decides to leave. She walks out as everyone stares at her, she is completely oblivious to the fact that just a few moments ago, bullets were flying everywhere and people were dying. She must of been blind and deaf, because without that excuse her behavior definitely qualifies as Too Dumb to Live. That or this is nothing new to her.
Eye Scream: Poor Sands. If you want to know, he got his eyes drilled out, and near the end we get to see his empty sockets. Fun. You get to see the approaching drill from Sands' point of view.
Fake Nationality: Antonio Banderas is Spanish, not Mexican. And Willem Dafoe is...really, definitely not Mexican, but this was lampshaded in the commentary slightly when Robert Rodriguez explains that he was purposefully playing it over-the-top.
Failed a Spot Check: Ajedrez fails to notice that Sands evidently has three arms. And to think he was the blind one.
Foreshadowing: Sands tells the boy selling gum that he "...never want[s] to see your face again."
Fun T-Shirt: Sands wears a great variety of obnoxious tourist-y t-shirts throughout the film—Johnny Depp thought the character would be the type to wear them and asked his sister to look around her hometown in Florida for the worst ones.
Gratuitous Spanish: Most of the dialogue is presumably in Spanish via Translation Convention, but some words are kept in Spanish, presumably for flavor, or for words that don't carry their connotations through a translation.
Groin Attack: Done to two mooks during Mariachi's escape from Marquez's compound by grabbing and twisting. OUCH.
Guns Akimbo: While not as prominent as the movie's predecessor, the Mariachi does do his share of this, often with different guns in hand rather than a matched pair.
Handicapped Badass: Sands, who is evidently willing to let mooks take potshots at his limbs just to echolocate them and blow them away.
Kick the Dog: Sands' henchmen shoot the old guitar-maker for no discernible reason. Sands himself shoots the cook of a restaurant because he cooked Sands' favorite dish too WELL. His reasoning was that if this one guy cooked it so great, Sands would never enjoy it cooked by anyone else, so he kills him to "restore the balance".
Revenge: Key motive for El Mariachi and Ramirez. Also, arguably, for Sands towards the end.
Reverse Mole: Ramirez bribes Billy Chambers into a Heel-Face Turn by promising that he would be allowed to return to the United States. He lied. To be fair, he wasn't lying out of villainy. He just didn't have that kind of power anymore. Had he lived, it's possible Sands could've worked out a deal for him.
Torture Always Works: When Ramirez gets captured, a pair of mooks discuss if they should torture the ex-FBI agent. One argues against it: "I was tortured once. I didn't like it. You know what the really fucked up part was? They tore out my left nut. That really turned me off to the whole thing."
Actually, he kills when he finds a chef who cooks it TOO well. Sands is obsessed with the idea of "maintaining the balance" in Mexico, which involves screwing up the nation's politics as well as its restaurant industry...
Un Installment: Inspired by the realization that many viewers of Desperado did not originally know that the movie was a sequel to El Mariachi, and thus were confused by the numerous unexplained but obviously important flashbacks, this movie includes many references to important events that took place in the third movie such as the murder of El's wife and daughter.
Cheech Marin also played a character that was killed at the beginning of the second movie and comes back here. It's confusing since he knows about the Mariachi's legends and sports an eye patch (the other character was shot in the head) but it is indeed a different character. Word of God states that he was originally supposed to be the same guy since Robert forgot he was killed and had to be reminded prior to filming.