Animations are a problem...
Currently, the only publically loader that I know of that supports animations is the OpenFlight loader from the guys at FullSail (and that is probably the most full-featured loader out there), and possibly the Neverwinter Nights loader.
Discussions with various people seems to indicate that Loaders end up being a "roll-your-own" if you really want to get all of the features that you need, like animations. Or convert all of your 3d models to OpenFlight format (and buy OpenFlight!)
Personally, I would pay good money for a Java3D Loader that supports animations, multitextures, and skeletons for either 3DS or OBJ format. It's either buy it, or hire someone else to build one, because I have too much on my plate already to spend the time to build it myself.