My thermostat will not allow me to lower it below 99 degrees, what should I do?

What is the make and model of the thermostat? Does it have a reset option? You could try removing the batteries, then locating the breaker that provides power to it (assuming that it is hard wired with battery backup) and shutting it off... wait, I would say, 10 minutes or so, then flip the breaker back on.

Anything? First start would be to locate the made and model and do some Goggling, but this is just what I would try, myself without any other information to go on.