I always thought we started fluoridation of water so the Soviets couldn't figure out how much uranium (and later plutonium) we were producing. UF6 is a bi-product of uranium enrichment and it's fairly straight-forward to estimate how much we're producing by taking water samples at the mouths of various rivers. But if everyone is brushing their teeth with fluoride, then it's a lot harder to accurately measure how much is due to enrichment.

This is very clearly a conspiracy theory, but water fluoridation is one of those topics that seems to attract them.