I am looking to develop an something that measures the distance between one "main" transmitter/receiver and one (possibly several) secondary transponders. It will need to be able to constantly track distance of the transponders in the case that the transponder is moving.
You can use some US distance sensor, and modify its library to look for multiple echoes. The time between the transmitted ping and the received echo gives the distance of an object.
If you use ultrasound, you've got a problem that all the signals will be at the same frequency; without some smarts, it will be impossible to distinguish transponders. You need to firm up your requirements, like accuracy, update rate, range etc.
Radio time of flight is out of the question.