Quarto has posted some interesting pictures of one of Prophecy's hidden models. The Copernicus Class Planetological Research Vessel was left behind in the game's data files, though it isn't automatically accessible. Using regular modding tools to attempt to swap in the design normally results in errors, but Quarto and Killerwave conducted some successful experiments on forcing the ship into the game. They managed to get it cruising, but some solid parts of it can be flown through, and there are a few associated graphical glitches. The research vessel looks pretty neat, and it's also always very interesting to see the differences between a ship's FMV version and in-game model.
I suppose I can upload it to KW's page if anybody's interested... but keep in mind, it's not something that I'd consider good enough to use in a mod or anything like that.
Edit: The ship was released for download on November 22, 2005 here. LOAF has also completed a detailed historical file for the vessel here.