In the episode "Black Bot the Pirate", Dr. Robotnik used the Robot-Transmogrifier Ray on Black Beard to transform him into none-other than Black Bot the Pirate. Once roboticized, Black Bot was completely loyal to Dr. Robotnik.
Dr. Robotnik used his ray on a whale in the same episode which then swallowed Sonic and Tails. While inside the whale, Sonic and was able to rearrange some chips in the whale's computer brain to make it loyal to him.
Dr. Robotnik uses the ray again in the episode "Prehistoric Sonic" where he uses the ray to roboticize a few different dinosaurs.
It is unknown whether there is any way to reverse the roboticization effects of the Robot-Transmogrifier. Sonic and Tails leave the whale as a robot and Black Bot the Pirate gets cut to ribbons.