Fire-breathing is an easy one.
The Pokemon holds a variety of non-harmful chemicals in flame sacs found within the mouth or throat, closer to the trachea. Upon using a flame attack, the Pokemon releases a portion of the chemicals, which mix together to form a combustible mass which is to be depleted after the attack. The Pokemon exhales a great deal of air in order to set the mass ablaze and direct the fire in the desired direction. Some Pokemon should have the ability to inhale while also exhaling, owing to their apparent ability to sustain fire-breathing for long periods of time. The inside of the mouth or, I guess Skuntank's butt, should be lined with resilient epithelium that resists the intense heat given off by the attack or regenerates at a rate faster than it can be destroyed.
- - - - -
For Regice, Regirock, and Registeel, I think it would be reasonable that they have some sort of conductive material inside that functions like the human nervous system, but not necessarily an entire body inside. The Pokemon should also have an energy-filled core from which it draws power from during times of need. Otherwise, it would draw from magnetic fields around the world, explaining the fact that it can use Zap Cannon, and other electrical attacks.