I tired it use my A/C and it would not come on. No fan, no condenser, nothing. Then about 2 weeks later it just kicked on like nothing was ever wrong, it worked just fine for about 3 days. Now, again nothing is working. I can't get the heat, A/C, or fan to kick on. Sometimes the thermostat will make the clicking noise, sometimes it won't. The thermostat is only about 6 months old. Anybody got any ideas?

Check the circuit breaker for the furnace and A/C. Check the fuses outside for the A/C.

That was the first thing that I checked. Could it be the wiring between the thermostat and the units? If so how would I go about checking them?

Turn on the thermostat and wait for the delay. See if you have 24 volts to the green and yellow terminals in the furnace, I'm going to take a guess the problem is a loose connection in the stat' check the red wire good.