The Mosquito Coast by Paul Theroux (1981) — A novel about an obsessive American who drags his family to the Honduran jungle to build his utopia. Dark, funny, and prescient. Made into a 1986 film with Harrison Ford. Still the most vivid piece of fiction set in Honduras.
Honduras Handbook by Chris Humphrey — A thorough practical guide covering the whole country including the Bay Islands and Copán. Dated in places but useful for background.
A Guide to the Birds of Panama: With Costa Rica, Nicaragua, and Honduras by Robert S. Ridgely and John A. Gwynne — The standard regional birding reference. Honduras sits in a migratory flyway and has exceptional birdlife; this is the book to have.
Gringos in Paradise: Our Honduras Odyssey by Malana Ashlie — A memoir about relocating to Honduras from the United States. Useful for anyone considering a longer stay.