Bioluminescence Is Cool

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Pretty, isn't it?

A Science Fiction trope: when writers think up alien lifeforms, there are several ways to make them cool, but nothing beats making them glow.

Examples:

Film

Avatar: Most lifeforms on Pandora, including much of the vegetation, have bioluminescent cells. The Na'vi have them as markings that form lines, which according to the background serve as a means of identification. Most plants, along with small animals, have a lot of bioluminescence, with larger animals and trees having less, although everything seems to have at least some.
The aliens from The Abyss.
Justified in Pitch Black due to the Bizarre Alien Biology of the light-sensitive monsters that eat everything else on the planet during every eclipse. The glow-worms end up saving the lives of the survivors.
The aliens from Monsters.
The Moorwens from Outlander.

In Kraken, the Krakenists believe that after they die, they become bioluminescent cells on the body of the squid god.
In "Dark Life" by Kat Falls people who live on the bottom of the ocean for extended periods of time often develop a bioluminescent shine from eating certain species of fish.
Wayne Barlowe seems to like this trope, given that he was a creature designer for Avatar and he wrote and illustrated Expedition, the book that Alien Planet was based on.

Darwin IV: Several of the alien species on the planet.
The Future Is Wild
The Most Extreme had the episode "Night Lights", which was all about finding the most extreme bioluminscent creature. The female angler fish won
During a brief period of unemployment, Sheldon from The Big Bang Theory mentions trying to engineer some bioluminescent goldfish (specifically to serve as an energy efficient pet/nightlight). It doesn't really come up again after a throw-away gag at the end of the episode, but he was successful in creating at least one.
In the Tracker pilot, Mel catches a glimpse of Cole glowing,something connected to his Cirronian nature and whatever he was doing in the bedroom at the time. (not *that*!)

Usually in any dungeon crawl situation, there are caves that have bioluminescent moss or lichen growing on the walls/floors.

The hanar race from Mass Effect. They communicate via patterns of bioluminescence.
- As do the Underlost from Septerra Core. That said, most of Shell 7 is covered with bioluminescent plants/fungi, serving as the primary source of light IN that layer.
The Macalania Woods in Final Fantasy X.
Definitely noticeable in Star Fox Adventures, which is arguably similar to Avatar in its visuals.
The Slylandro in Star Control II
Zangarmarsh and Vashj'ir in World of Warcraft
The Forest, and the creatures who live there in Crea Vures. Interestingly, the bioluminescence on the eponymous CreaVures also serves as a representation of your health (with it fading for a while if you're hit), and sometimes as an indication as to whether an aggressive animal is cowering or not (with theirs fading for a bit).
Everything in the Deluded Depths. Even Alice's dress has an angler and glowing dots and stripes.
Glowing Fungus in Fallout: New Vegas in multiple colours. Some are edible.
In Terraria, you can find Blinkroot hidden underground, which does exactly what you'd think it does: Blinks. (Though only when it's blooming.) Also to be noted are tall Glowing Mushrooms, also found underground, and better for healing and potion-making than surface 'shrooms.

in Bionicle: The Mask of Light, Takua gets distracted by some glowing coral-like structures. He immediately puts them on his head and starts hopping around like a flourescent bunny rabbit.

The protein Luciferase and its relatives are the cause of natural bioluminescence, for example in fireflies. It has been put into other creatures to create glowing bacteria, etc.
- A more famous but unrelated protin is GFP (abbreviation for "Green Fluorescent Protein"). Its derivatives have been established as common tools for scientific research. It's not true bioluminescence: the protein is merely fluorescent, so it only glows under a light source.
Ravers and CyberGoths have a liking for glowsticks and clothes that imitate bioluminiscence. While it's definitely running off the Rule of Cool, there's also a functional reason behind it: Supposedly, the glow from these sources have a soothing effect on the mind, reducing the chances for a Bad Trip. Considering that these subcultures have a particular leaning towards psychedelic substances ...