I've been thinking about doing a pirate ship, something like the Black Pearl but maybe a heavily bashed kit of some existing ship. At any rate in the train hobby I have done a lot of lighting and effects. For a base to the light system for a ship, I'm thinking of using the
Woodland Scenics Just Plug lighting system. I used it on my latest train layout and it works fantastic. It's pretty much plug and play if you're not a techie. They have some pretty nice porch lights in O 1:48, HO 1:87, and N 1:160. I'm thinking the smaller ones could be fashioned into desk lanterns on a 1:50ish model. The nano lights are tiny so would be easy to hide. They also come in different colors so you can get a nice yellow effect.
One nice thing about the just plug system is it comes with built in dimmers for the lights. Typically leds are way brighter than needed unless you do a lot of playing with resistors to get the intensity you want.
There are quite a few train suppliers that make circuits that simulate a camp fire and arc welders. These circuits could be used for a stove and the arc welder for a lightning effect in the case.
Circuitron (Page 41 of thier catalog) is a company I've used a lot of products from. If you search for "model train campfire circuits" or Arc Welder Circuits there's tons of do it yourself stuff out there, schematics etc. For the US ngineering.com has tons of leds and resistors etc. These lights can turn into a hobby of their own. In my experience by the time you buy all the parts to make this stuff yourself the Just Plug system starts to look pretty reasonably priced.
Also depending on what scale your working in, don't neglect looking into fiber optics. These Christmas lights are all hooked to one white led. The color is from different colored fibers. The house is about 20mm tall. Could probably make a candle or lantern with 1 fiber. Just made me think about building a candelabra in the captians cabin.