Most of the animations of cars, flying saucers, robots, etc. I'm creating for Xion the same way sprites are created.It's just on a larger scale and much simpler.
Using a 3d modeling program, rather than a paint program, the model of choice is manipulated against a high contrast background.(Pink is usually easiest, just like sprites.)
Screenshots are taken for each animation frame and then opened in Photoshop to be placed in animation sets.
Animations can be built effortlessly this way, compared to painting frame by frame.Although I'm rendering them fun and sketchy right now, very realistic effects can be achieved w Lightwave, Maya, etc.
(On a side note, Viewpoint, the modeling tool I use frequently, allows individual parts full transparency control, which comes in handy.)
Any modeling program that lets you specify a background will work.
Most Game Editors can be used in ways like this.It makes Photoshop a little more interesting, too.