Birdcaged

It appears The Hero has found himself captured. But where would the evil overlord put him? Seems a regular prison isn't around or just wouldn't do.

So the bad guy sticks The Hero in a birdcage. This is usually done both to legitimately keep him locked away and to taunt him. On some occasions, the animal may be kept in the cage with the hero. Note that it doesn't necessarily have to be a birdcage, but is the most common form of this trope.

This becomes even more common when a character is shrunk or otherwise much smaller than their captor(s).

Examples of Birdcaged include:

Anime and Manga

In the "Alfheim Online" arc of Sword Art Online, Asuna's consciousness/avatar is imprisoned in an inaccessible golden birdcage by her megalomaniac arranged fiance.

Comic Books

In one Golden Age Justice Society of America story, Hawkman is shrunk and placed in a birdcage.

Fan Works

In Mega Man: The Series, a shrunken Mega is placed in a hamster cage.

Film

In The 7th Voyage of Sinbad, the shrunken princess is kept in a birdcage.
On The Adventures of Baron Munchausen, The King of the Moon puts the Baron and Sally in a birdcage, where they find the Baron's old friend Berthold.
In Valiant, the one captured in the first few minutes of the film and Bugsy were, naturally, imprisoned in a birdcage. Justified as they are birds and all.

Literature

In the Artemis Fowl series of books, one bloodthirsty villain gets his mind trapped into the body of a hamster. He is then put into a small cage, where scientists throw toy swords into the cage and watch him try to pick them up.
In The Hollows, Rachel Morgan gets turned into a mink, and stuck in a cage.
When Tristran gets turned into a hamster in Stardust, this happens to him.

Live-Action TV

The Doctor Who series 3 finale.
Happens to Tony and Roger in a episode of I Dream of Jeannie.
In Fraggle Rock, a shrunken Mokey is placed in a dollhouse.

Tabletop Games

Dungeons & Dragons. The Prison of Zagyg was a magic item in the form of a small birdcage. When the command word was given, the victim was shrunk to 3 inches high and stored in the cage.

Video Games

In Scribblenauts and Super Scribblenauts, you can do this to anyone you shrink.
In Monty Python's The Meaning of Life The Videogame, there is a group of sailors who are trapped in a birdcage.

Western Animation

In the Teen Titans episode "How to Make A Titananimal Disappear", Raven is turned into a rabbit and then housed in a birdcage.
Not only is The Tick (animation) shrunk and put in a birdcage, he is also turned into a two-headed bird that speaks French.
In The Avengers: Earth's Mightiest Heroes one of the maximum security prisons for supervillains is like this. They are shrunk using some of Hank Pym's technology, so the prison is small enough to fit on a large table.
Adventures of the Gummi Bears episode "A Gummi in a Gilded Cage" sees Sunni captured and stuck in a birdcage to serve as the Vulture King's 'songbird'.
the Lion King: When Scar takes over Pride Rock, he traps Zazu inside an animal's ribcage.
Stromboli puts poor Pinocchio on a cage to keep from going back home.
In The Secret of NIMH, Mrs. Brisby is caught inside the farmhouse and put in a birdcage. She makes a daring escape after learning that NIMH is coming for the rats.
Fievel is put in a cage in An American Tail. He is taken out after befriending his jail guard, Tiger.
In the Chip 'n Dale Rescue Rangers episode "Zipper Come Home", Chip, Dale and Gadget are trapped in a bird cage by a tribe of beetles, and placed near a rising river that threatens to drown them if they don't get out in time.