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Facetiae
This word is the plural form of the Latin facetia, meaning a jest or joke.  According to the OED the English word means "witticisms" or "humorous sayings."  [JC]

Fiat
Literally means "let it be done" in Latin.  However, in English it has come to mean a command or decree.  [TH]

Forte
From Latin, "strong." Comes in English to refer to a person's area of special ability or expertise.  [JM]

Genius
The Latin word genius refers to a person or place's guardian deity.  In English, the word comes to refer to a person's particular talent or inspired power.  [RR]

Gratis
This Latin word means "free" or "for nothing" and has retained the same definition in the English language, even today.  [MD]

Hippopotamus
Greek hippos, "horse" + potamos, "river". 
OED  [JM]

Honorarium
An honorarium in Latin is a voluntary contribution to the treasury or a compensation for services.  Today honorarium means a reward or a payment for services rendered.
OLD
OED  [KD]

Incubus
From the Latin word incubare which literally means "to lie on," this word means something that "lies on" someone. In English, it has also come to mean a nightmare or a thing which weighs down upon an individual. It is cited by the OED as occurring as early as 1205.   [MD]

Innuendoes
Innuendo is a Latin gerund literally meaning "by nodding."  In English innuendo was incorporated around 1564 for use in legal documents to introduce a parenthetical explanation.  By the 17th century, innuendo was used to refer to any hint that implies more than it says (especially of a derogatory nature).
OED  [KD & RR]