An emperor was a male monarch and an empress a female monarch. The title was typically held for the sovereign ruler of an empire. The female version sometimes indicated the spouse of an emperor. The title was held to be of a higher rank than that of a king or queen.
The Romulan Star Empire was ruled by an emperor, as was the Klingon Empire on the return of Kahless.
Muro III was the Emperor of a planet in the Delta system in the 17th century. (TOS comic: "The Haunted Asteroid")
Emperor Djan was the Emperor of Nukolee in the 23rd century. (TOS comic: "A World Gone Mad")