Queen

A Queen is a female monarch that is the feminine equivalent of a King. Throughout the world, Queens appear to be just as powerful as kings, or in some cases, even moreso, with some kingdoms only being ruled by queens.

Friendship is Magic
was the ruler of the Changelings for an unspecified period of time. It's possible that the tradition of Queen rulership in Hippogriff civilization dates back many thousands of years as well, as Hippogriffs were among the oldest civilizations in all the world, and had unified governments long before any other civilization. After and  passed rule of Equestria over to her,  was referred to as a queen, specifically Queen of Equestria.

IDW
The oldest known Queen was Queen Cleopatrot of the (presumed) Anugyptian kingdom who ruled thousands of years prior to the Fateful day. Cleopatrot appeared to be held in just-as-high regard as another Anugyptian monarch named "King Anubis". Unlike Anubis, Cleopatrot didn't appear to be a cruel and unreasonable ruler, but still appeared to be selfish in her own regard.

A handful of minor kingdoms within Equestria also appeared to be ruled over by queens, such as Trottingham, which was ruled by the evil Queen of Trottingham (though this queen in particular may have been fiction). Although not confirmed, the Kingdom of Thicket may also have a queen, as King Aspen showed up with a female companion to the Convocation of the Creatures event on Mount Metazoa.

In The Mysterious South, the kingdom of Abyssinia was ruled by a ruling family of both king and queen, both of whom seemed equal, though the queen's more assertive, brave and intelligent personality may have made her the "dominant" monarch.

Despite being a Princess, has been referred to as a queen before, (albeit, in apocryphal material that may not be canon), meaning the difference between Queens and Princesses, at least in Equestria's royalty, may be a name one only.

"Empresses" appear to be the equivalent of queens.

My Little Pony

 * Queen Bumble

Friendship is Magic

 * Queen Chrysalis
 * Queen Chrysalis (IDW)
 * Queen Chrysalis (Mirror universe)
 * Queen Cleopatrot (Anugypt)
 * Queen of Trottingham (Trottingham)
 * Rainbow Dash
 * Abyssinian Queen (Abyssinia)
 * Queen Novo (Mount Aris/Seaquestria)
 * (Equestria)

Appearances

 * (as "story queen")
 * Tails of Equestria: The Official Movie Sourcebook
 * (as "story queen")
 * Tails of Equestria: The Official Movie Sourcebook
 * Tails of Equestria: The Official Movie Sourcebook