In 1999, Japanese researchers developed the Robo-Roach, a living cockaroach who's movement could be partially controlled using a radio transmitter.
One could imagine that within a few years, researchers could take advantage of existing technologies, such as automated microelectronic design and genetic engineering, to streamline and improve the circuitry currently on the insect, giving them more and more control. Eventually, with nanotechnology, they could literally grow the circuitry on specific parts of the brain, giving them complete control.
In addition, they could put miniature computers in the bodies of the cockaroach, and use those to automate the roaches' movements. In this way, they are able to program an army of robot cockaroaches that behave in predefined manners, without having to control each individual insect.This research would of course be extended to other animals. Mice, rats, rabbits, and monkeys would all be subject to electronic tampering by researchers. Behavorial researchers could see what happens when a robot mouse interacts or interferes with regular mice. Zoos could let visitors "control a monkey", swinging from branch to branch with a controller. Even if the general public balks at such an idea, such applications would thrive "underground". Cockfighting is immensely popular as it is - giving humans control over the animals would doubtlessly be even more so. Hunters may enjoy taking on a super-bear that provides more of a challenge than a regular bear, but is far less dangerous, since it would be programmed not to harm the hunter.
Those familiar with the novel "Jurassic Park" should remember its cautionary message - "Life finds a way". Even though we think we have complete control, this is rarely the case. These engineered animals could spontaneously evolve and not only retake control of their own bodies, but take advantage of the technology implanted within them. An evolved animal that combines an instinctual animal brain and the high-speed mathematical coprocessor could even surpass humans intellectually. The super-bear, for example, may really become a super-bear, with enhanced physical and intellectual capabilities. This bear could then train other bears, modified or not, and "rebel" in some way. The animals could communicate and interact in new ways that we never imagined.
Alternatively, the on-board computers could somehow enmesh themselves with the host animal's consciousness, and become self-aware, with similar results.
In the end, this is another example of control versus out-of-control.