I've been working with irrlicht for a few weeks, but I've ended up doing quite a bit of coding around it rather than actually using it for anything other than rendering. I'm currently running into odd issues with it's support for skeletal animation, and I'm sure with time I could find a solution (or code one in a longer amount of time). But rather than do that, I'd just like to know:

Is there a graphics engine or library with a feature rich/well developed skeletal animation system? Preferably one that allows 'manual' bone transformation (as in from code). Language isn't an issue, but C/C++ is preferred.

Have a look at Horde3D, it has a solid skeletal and morph animation system which support multiple animation layer and manual joint transformations (a joint is a regular scene node which animates the bones of the model)