A few ideas have been floating around my head recently. With the current lack of entity modelling in the java version of Minecraft, I have been thinking about basic workarounds for this problem.
Mobs – certain mobs will be easier than others, but the general gist is to texture parts of the mob invisible (head and arms will be easiest to replace) and giving the mob models in it’s hands or on it’s head which are then rendered as the mobs arms or head.
Chests – trapped chest will work best as you can detect whether it is open based on the redstone signal output. Placing an entity on top of the chest with the model be rendered on the entity ie placed in the entity’s head, using the redstone output to allow for a different model to be rendered when the chest is opened.
Boats – with the ability to have two passengers in a boat, one of them could be an entity with a model renedered on it, with the other being a player this would allow for such things as small airships which the player can actually fly.