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I think the colloquial way (and most common way) is: 頭が痛い。 Or even more colloquially dropping が: 頭痛いよ。 Please note that 痛い is an i-adjective so 「頭が痛いだ。」 is not correct. This can be used for other body parts too. I think that the confusion is because in English there are words for some of the "aches" which you often use, like "headache" or ...
You have a couple choices: 頭が痛い （not ×頭が痛いだ） 頭痛がする I basically agree with Szymon's answer that 頭が痛い is more colloquial and all-around more common. You can use either phrase, though. (You can make it more colloquial yet by omitting the particle が.) Adding だ to adjectives like 痛い is nonstandard. To make these more polite, use 頭が痛いです or 頭痛がします.
This may serve as an interesting read. It seems to be a list of the license plate numbers that people wanted, sorted in order of frequency. Unfortunately, frequency lists are very difficult to find because they require large amounts of information to be accurate and few people have the resources to gather and subsequently analyze that information.
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