These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Animation Age Ghetto: The one star reviews on Amazon.com are full of parents complaining about this PG rated film being not suitable for children.
Big Lipped Alligator Moment: At one point when the characters are traveling underground a giant eye opens and watches them walk away. One character remarks, "That's a big one," but nobody else even notices it. It's never explained and never appears in the movie again.
There's also the dance when the town goes to get water after the bell rings. Granted, we are informed that getting water on Wednesday is a regular ritual - the dance itself, though, comes out of nowhere and it's never explained what it has to do with anything.
Foe Yay / No Yay: Jake's behaviour towards Beans. In his first appearance, Jake almost strangles her and licks her face. And in another scene, he almost strangles her again.
Harsher in Hindsight: This was ILM's first animated release, and it was both successful commercially and competitive enough to win an Academy Award. It looks like it will also be ILM's last, as Disney bought Lucasfilm, which includes ILM, and is unlikely to give them a shot at doing more animated films in the future.
When Rango leaves Dirt, returns to the road, picks up Mr. Timms and hugs him like a child would a security blanket or stuffed animal.
Ugly Cute: Rango is basically a photorealistic anthropomorphic chameleon, but with that little Hawaiian shirt he's sporting and his constant freakouts, how can you not love him?
Real life chameleons are not that ugly.
Priscilla is pretty adorable too. Along with Ambrose and possibly Ezekiel, she's one of the closest characters to being traditionally cute.
Waffles the horned toad is red-eyed, spiky, and nearly toothless, and is one of the cutest characters in the film.
Beans has some undeniable appeal as well.
Uncanny Valley: It's a tad jarring to see a bunch of eerily realistic animals running around in clothes and talking, but it was obviously done as a stylistic choice, similar to the illustrations of storybooks featuring animal characters in very human situations.
Visual Effects of Awesome: Just about all of the animation in the film is fantastic. Naturally, it's from Industrial Light and Magic, who have only ever done fully realistic effects before this.