Although there are no regular passenger ships to or from Honduras, it's often possible to arrange passage with a fishing or cargo vessel if you pay your way. Negotiate directly with the captain. On the Pacific coast, try San Lorenzo to find boats to Nicaragua or El Salvador. It's easy to fly to any of the Bay Islands from La Ceiba, Tegucigalpa and San Pedro Sula, and to fly among these three major cities. More air routes into the Mosquitia region are making that remote area much more accessible.
Trains are slow, rudimentary and very cheap.
Services have been disrupted in the past, so check whether the trains are actually running before planning to use one. Boats are common modes of transport between the Bay Islands and along the Caribbean coast, especially in Mosquitia, where there's just one road. There are plenty of taxis in most towns but they are not metered, so negotiate a fare before you get in. Car rental is available in main towns and the main roads offer excellent driving. Hitching is generally easy in rural areas, where trucks often stop to pick up passengers.