Mysterious Animal Senses

Whenever animals are used as protagonists in a story, it's nearly guaranteed that they'll possess senses at least on par with, and more likely far in excess of, the human norm. Also, all animals will have very nearly the same set of senses.

A wolf protagonist? Not only can he discover your life history from one whiff of your clothes, he can also tell what color hat you're wearing from a mile away, and hear the sound of snow falling through a half foot of steel. And probably be able to sense ghosts and the innate innocence of The Messiah, to boot.

This is not... exactly how it works in Real Life.

While many animals do have interesting and novel abilities, they also tend to lack some of the senses humans consider to be completely mundane - tri-chromatic vision most obviously (but not exclusively). And no single animal has all the nifty keen abilities you saw on that one Discovery Channel special.

See also Super Senses and Animal Eyes. Compare Sense Freak. Super-awesome animal-like senses are often employed as one of the reasons why Our Elves Are Better (Petting Zoo People as well) and the lack of those makes humans Puny Earthlings in comparison.

Subversions and aversions only, otherwise we'd have every critter book in existence here

Literature

 * Averted in the Silverwing series - the bat main characters view the environment almost exclusively through echolocation, and colors besides silver are essentially never mentioned.
 * This was actually deliberately done by the author, and it is not something you notice until you know. (Also, in this case, "silver" probably refers to reflective gray.)
 * Spoofed in the Discworld book Moving Pictures, where the talking Holy Wood animals are annoyed that Victor keeps referring to them as having "mysterious animal senses".
 * Gaspode the Wonder Dog is also rather put out to find that he's seeing in color. All of a sudden, the pleasantly gray meat scraps he'd previously enjoyed are all icky red/maroon stuff!
 * Animorphs usually put a lot of (relatively believable) detail into the differences in the way the protagonists' senses worked in their various animal forms.

Tabletop Games

 * Each Species in Ironclaw has one or two Natural Senses, but no more; when using those senses, they can include their Species Trait in their Observation roll. Some Species have Gifts that improve those sense even further (Keen Eyes, Keen Ears, Keen Nose), or provide exotic sensory abilities like Echolocation.

Web Comics

 * In Kevin and Kell, it's occasionally mentioned that Kell (a wolf) is color-blind, and characters are frequently shown perceiving the world primarily through scent.

Web Original

 * In the Whateley Universe, after Merry gets turned into a werecat, she goes color-blind.
 * In Darwin's Soldiers, Dr. Kerzach, a anthropomorphic cassowary has pretty much no sense of smell.
 * Also, snakes have poor hearing.

Western Animation

 * When Momo the lemur's POV is used in Avatar: The Last Airbender, the view is bubble-distorted and tinted green to show less nuanced color vision and a wider visual range. There's also the Shirshu, that uses scent alone, which is shown as different color trails on a grainy black background, and pouring a bunch of perfume next to it made it entirely disoriented.
 * The Simpsons and Rugrats also use odd visual filters when using an animal's POV on occasion.

Film
"Donkey: Blue flower, red thorns, blue flower, red thorns...oh, this would be so much easier if I wasn't colorblind!"
 * Shrek


 * While wandering frantically through a bunch of hedges with blue flowers and red thorns, for those who haven't seen the movie.
 * A similar joke is used for a Wire Dilemma in Cats and Dogs.

Real Life

 * In a non-fictional subversion, bats were variously hypothesized to possess either phenomenal night vision or (once blindfold experiments shot that down) a sense of touch so keen that they could feel distortions in air density from nearby objects. Only when earplug tests revealed they needed to hear to navigate was the mystery of their Mysterious Animal Senses (echolocation) solved.

Video Games

 * Sam & Max Hit the Road: The two main characters (a dog and a rabbit) purchase a paint-by-numbers game only to find out neither can see in color.

Web Comics

 * In Freefall, though the protagonist (a genegineered wolf) does have superhuman smell, she must defer to human as to what are "good" smells ("Decaying Buffalo... There's a scent that... Well... You just want to roll in it."). She's also colorblind, and mentions that she hears in a different range to humans (shouting to overcome a high-pitched noise her coworkers can't hear, for instance).
 * Example for colorblindness shown in this strip: "It's always difficult trying to appear attractive to a sense you don't have".