In the southern US, the only natural way to say this sentence would be "half of six is three". "One half of six is three" is technically correct but sounds stilted. The only time we would say it that way is if one half were being compared to another fraction, like "Three halves of six is nine, but one half of six is three." "The half of six is three" is simply incorrect.
In the UK, "half six" without "a" and "of" is also acceptable, which I often hear. "Interestingly, we also use “half” without “a” in other situations, and not just when we’re giving the time. For example, if I eat half an orange – that’s how I say it! ...": http://www.bbc.co.uk/worldservice/learningenglish/radio/specials/1535_questionanswer/page63.shtml