These are very interesting questions! I am having trouble finding out why dogs' eyes change color, but the basis for permanent color change in human eyes may be similar.

In humans, melanocytes are cells that produce pigments for eyes, hair, and skin. One of the major pigments produced by such cells is called melanin. As children develop, the amount of melanin their melanocytes produce may change over time, thus resulting in a change in eye, hair, and skin color.

Fish and other organisms that change the colors of their whole bodies, on the other hand, can often do this in a reversible manner. Often, the reason for this kind of color change is for amouflage -- either as protection from predators, or to trick prey into coming closer. I hope this helps!

Fish can change color for a number of reasons, and it depends on the fish. Fish containing bioluminescent bacteria can make light (or rather, the bacteria make light, and the fish just hosts them).