Fantastic Nature Reserve

Safely guarded from the Muggle world that's so ignorant and hostile to it, the Fantastic Nature Reserve is one of (if not the) last refuge for mythical beings. Much like the Bazaar of the Bizarre, the Fantastic Nature Reserve will have many species of flora and fauna heard of only in myth and fairytales. Entire ecosystems may be preserved in lush "biomes", or individual beings kept in cages much like a zoo (which is likely to also have an evil Zookeeper).

It may be hidden somewhere deep in the dark, forgotten places of the world, in the labyrinthine corners of human city thanks to some powerful illusions, Another Dimension entirely, or even bravely visible to the world at large. If it's hidden, that's because there is safety behind The Masquerade as a Hidden Elf Village, and by banding together they can cooperate to fend off those pesky humans. If out in the open they may hope to survive by raising awareness of their existence, which may be exactly what's called for it the residents are subject to Gods Need Prayer Badly and Clap Your Hands If You Believe.

Another possibility is that the residents have formed this Reserve because Mana is a part of their "diet," and with it becoming scarce in the Muggle world they have to seek sources of magic and live near them. Because of this the Fantastic Nature Reserve is likely a settlement on the magical equivalent of a proven well. If this miniature Cosmic Keystone is stolen or destroyed, the Fantastic Nature Reserve will fall with it. Whether natural or artificial, the Fantastic Nature Reserve residents are likely fiercely protective of the place, its residents and its secrecy. Unless of course they're not there of their own free will.

It's also possible for a Fantastic Nature Reserve to be "person" made. A benevolent "zoo keeper" likely does this to preserve the Uniqueness Value inherent in these creatures and to protect them from poaching. The less altruistic Collector may justify objectifying these creatures (whether sentient or not) on the basis that they're saving them from destruction. An outright evil zoo keeper will use them as shock troops and as a self-replenishing treasure trove of magical ingredients. It's easy to harvest Eye of Newt when you can apply Healing Factor laden troll blood to keep the newt from going blind.

Anime and Manga

 * The Count's shop in Pet Shop of Horrors is played up as one, even if he does occasionally sell some of the residents. Luckily, the residents typically volunteer for this so everyone is happy in the end
 * The Headmaster in Rosario to Vampire has one of these in a pocket dimension, it's for monsters that could never adapt to the Masquerade.

Comic Books

 * The Farm in Fables (comics).
 * The Phantom has Eden, an island where even normally predatory animals are peaceful vegetarians, and live together with their would-be prey. Aside from the lions, dolphins, tigers (in Africa!), gorillas, etc., there are some miniature dinosaurs and a family of cave monsters.

Film

 * Midian in Nightbreed is the last city for the titular Nightbreed, who have been persecuted for all of human history.
 * Played for Laughs in Shrek, where all of the fantasy beings Lord Farquad has exiled are sent to Shrek's swamp.

Literature

 * Fablehaven is about a secret nature preserve protecting the beings of myth and legend from the outside world, complete with caretakers that act almost as park rangers.
 * The Forgotten Beasts Of Eld by Patricia a McKillip, where Sybel has a menagerie of legendary animals which she and her ancestors called using magic to their crystal domed white hall. Animals include a giant black cat that knows witch's spells, a dragon that killed many men, a boar that knows the answer to every question but one and a falcon that rode on heroes' arms.
 * It's implied it's how fantastic creatures survive in Harry Potter.
 * For John Hammond, Jurassic Park is this, even in theme park form. Lets just say it went horribly right.
 * Don't forget that there are two islands: Isla Nublar (the park) and Isla Sorna (site B).
 * The dragons are given these in The Last Dragonslayer.

Live Action TV

 * The BBC's Walking With Dinosaurs Spin Off Prehistoric Park fits pretty well. It involved a naturalist who traveled through time and brought back extinct animals for his nature preserve in Africa. Basically, a more down to earth and zookeeper-esque version of Jurassic Park... but with time travel !
 * Sanctuary is this trope.
 * A Sliders episode has a dinosaur preserve, the last place where they can be found on this world. Naturally, it's also a haven for poachers, provided they don't get eaten. Rangers are only allowed to enter the park via holo-projections, so as not to disturb the dinosaurs.

Tabletop Games

 * This is the premise of the Hollow World universe of Dungeons and Dragons, according to in-game mythology.

Web Comics

 * Order of the Stick has the pit full of monsters from previous editions, the intent of which wasn't so much to protect the beasties as to keep them away from harming PC's.

Western Animation

 * In an episode of Superman the Animated Series, Supes and Lobo are captured by an alien who keeps a collection of creatures who are the Last of Their Kind.
 * The irony is the alien hires Lobo to capture Superman before revealing that he wants the last Czarnian as well (Lobo is a self-made "last Czarnian", though, as he is responsible for Czarnia's destruction as part of his science project).
 * There are also some dinosaurs on the ship as well.

Video Games

 * Dracula in basically every Castlevania game. It's implied all of the creatures in his castle have died out centuries ago in the real world.
 * Pokémon has the Safari Zone.
 * Touhou takes place entirely within Gensokyo, a Magical Land that was sealed off from the rest of Japan in the Meiji Era, and explicitly exists to preserve the supernatural creatures who would otherwise die off due to lack of belief.
 * In Overlord II, the elves are trying to create one of these to save magical creatures (including themselves) from The Empire (the other Empire).
 * In Star Ocean the Second Story, Claude, Rena and the others must visit one in order to obtain a wild Psynard. The keeper is understandably reluctant to let them into the preserve, but accompanies them inside, and can potentially be recruited if the player wishes.