When the mayor tells Rango that "people need something to believe in", he isn't referring to Rango's heroism, but to his plot to use the townspeople's belief in Rango as a distraction to continue his plans.
During the scene where Beans is allegedly about to sell her ranch to the Mayor, she hesitantly reaches for a glass of water. This takes on a whole new meaning when you remember the beginning where Rango's ...Barbie doll reaches for the glass of water (representing a "chalice of poison") as part of his emotionally unstable princess story. We're given the same context, with poor Beans about to lose the very thing she loves most. But instead of taking the "poison", she throws it at the Mayor in defiance! This marks that as opposed to Rango's idea of the Damsel in Distress, Miss Beans is a real person who's willing to fight for what she believes rather than surrender.
Of course Rango is capable of playing those blistering flamenco runs on the guitar. What else is he going to do with his time? Truly an artist in all facets, amirite?
This one is in a Viewers Are Geniuses sort of way. Though this theory might be kind of a stretch, some scientists think that humans got the notion of dragons from our brains fusing our mental image of the main predators at an earlier point in our evolution together — snakes, birds of prey, and cats. On the scale that our heroes are on, snakes and hawks seem like dragons to them and, for the most part, that's how they act.
The Spirit of the West is more like the Spirit of the Western.
After Rango meets the Spirit of the West, Roadkill mentions that "we see what we need to see" in reference to the spirit. Rango needed to be a tough guy, so who better to take advice from on playing a tough guy in a Western setting than Clint Eastwood?!.
Another way of looking at it is that the Spirit takes on differing appearances based on what his viewers identify with the most. As an actor, of course Rango would see the Spirit as a Western actor that he would idolize.
Much like the Spirit of the West himself, Rango is also a "man with no name".
Notice how Rango breaks a fine bottle of water which is probably worth more than he is. Notice the Mayor not noticing? This could either be interpreted as Played for Laughs, or that the Mayor just doesn't care, given that he was hoarding the vast majority of Dirt's water supply.
In Rango and the mayor's first conversation, the mayor says that he's lived long enough to remember a time where the Mojave desert had flowing water. This answers a question not particularly raised: why are there so many mammals and other animals not indigenous to a desert environment living in it? Because long ago they did at one point have an environment suited for them, until eventually the water flow was directed elsewhere and the place dried up.
Rango is a chameleon, as well as an actor. What better vocation for someone who can physically blend into their surroundings wherever they go?
Horned toads are known to defend themselves by squirting blood from pouches near their eyes. Waffles has red irises. These two things most probably do not relate biologically in any way, but the latter is a possible reference to the first one.
When Beans asks Rango what his name is on the way back to town, he goes on and on about 'his stage name, pen name, avatar,' etc., and is still going on listing all the different types of names he supposedly has by the time they get there. This makes sense when you remember that, at that point, he has no name, and when faced with a weakness or point of discomfort, what does he do? He brags and blusters and goes on at length trying to build himself up with talk.
"All we got here is cactus juice." — Kids are likely familiar with stories of people in the desert getting water from cacti, but a bar might be more interested in peyote than ordinary juices.
During the extended ending, Rango explains that he has gun lotion in his bag, much like another cosmetics product related to guns: gun powder.
Right up until the Mayor calls him in to deal with Rango, Jake has been built up as this great hero-killer — he "never leaves without taking a bloomin' soul." In that confrontation, he does by exposing Rango's lies and forcing him to prove his 'one bullet' story, essentially killing the larger-than-life persona he'd built up at the start of the movie. Rango even drops the sheriff badge in the graveyard, and only gets it back once he realizes that he still is a hero.
On Wounded Bird's changing English skills: when we first meet him, he speaks in broken English, but throughout the movie, it gets progressively better. That isn't a Plot Hole. You could argue that the broken English is deliberate on his part to play into stereotypical images of Native Americans in Westerns.
The Super-Persistent Predator trope makes a lot of sense if you consider Metalbeak not as a random desert predator, but specifically posted to keep outsiders from reaching the town, and keep the townspeople confused and afraid. Someone gave it the beak-blade. After all, the hawk was "the only thing keeping Rattlesnake Jake away" from Dirt. The Mayor would need to stop Jake from interfering in his own plans until he needed him. Certainly the You Have Outlived Your Usefulness scene implies the Mayor was worried Jake would turn against him at a future point, and decided to get rid of his scaly partner while he was vulnerable.
I don't know? The Mayor doesn't seem to have any form of leverage. The bird can fly so getting water is way easier a task for it, and what stops it from eating the Mayor?
When first confronted by the hawk, Rango is told to blend in. He curls up on the ground and starts changing into a variety of bright colors while trying to do so. This might just make it seem as though he's just bad at it, but in reality, chameleons don't change colors to camouflage. They either become brighter or darker according to heat, or gain bold colors to communicate or attract mates. He's not bad at camouflage, he's just not meant to do it.
Rattlesnake Jake probably realizes the Dramatic Irony of the One Bullet story. He lambasts Rango for his one bullet story, proving he is a fraud for not shooting him with one bullet at point-blank range. When Rango's plan leaves Jake unarmed and defenseless, Rango reminds him that it only takes one bullet, something Jake realizes Rango is now very capable of doing. When the Sheriff is about to kill Jake with the gun Rango was using during their duel, it doesn't go off because it isn't loaded, because Rango removed the last bullet to use to escape the water tank, which not only leads to the Sheriff's defeat, but also saves Jake's life. With a single bullet, the very same that was going to be used to kill him, it saved Jake's life. It's why Jake tips his hat to Rango, because he, in a way, actually accomplished his story, making him someone worthy of his respect.
We're probably better off not knowing what Rattlesnake Jake has in store for the Mayor in the end. The guy is pretty much described as a hellspawn Grim Reaper. Even if half of that is just myth, he clearly has far worse in store than just killing him off and being done with it.
Rango was a pet at one point, to some human family who would have cared for him. How will they feel when they realize their pet chameleon was lost somewhere on what was a presumably long trip with no chance of ever finding him again?
It's mentioned that Jake won't leave town until he's taken a soul. Considering that he's a carnivorous snake, and that snakes don't eat as often as other animals, it's entirely possible that his payment for services rendered is dinner.