Here is the situation, 2 wall outlets, 1 fluorescent, and 9 celing cans all on the same circuit. 6 of the cans are controlled by a pair of 3 way switches, the other three on single pole switches. Nothing works. The circuit breaker doesn't trip and I have reset it several times. What happens is that everything will work one day, and then bam, out for a week or two until they mysteriously work again. When they aren't working, I've tested the wires to the switches and as expected 1 is hot, and the other not when the switches are removed. When I hook the switches back up, both of the wires on the switch become hot and the single pole switches will affect the wires on the 3 way switches actually making the lead wire hot or cold depending on the position of the single pole. What could cause this?

Could be a loose neutral wire. If the power can't make it back to the box through the white wire, no light. Since it is the whole circuit, I would open up whatever is closest to the box and check its connections. With the power off, he white should be continuous to the ground. With the power on, it shouldn't show more than a volt or 2. If it isn't continuos to ground, it could be loose at the box. To check that means taking the cover off exposing the main feed from the pole outside. Even with the main breaker off, the big wires running to it still have power. Think twice about messing around in there.