The one that gives the bonus to whatever attribute you want. Runes of the same type (ex: two fire runes) won't stack, but a rune WILL stack with the bonus on the head piece. (if you have the fire head piece and a minor fire rune in your armor, they will stack for +2). So go with the one that has the attribute you want to get the highest.
And you can put a rune in the head piece as well so that it gives +1 to two attributs (I don't know if a fire rune in a fire head piece will stack. Never tried.), but it doesn't really matter since elementalists can only use vigor, energy, and one or two elemetal magic runes (unless you are trying to spec in 3 or more magic lines in which case you are only hurting yourself) so I've never bothered putting a rune in my elementalist's head piece. Good for warriors, though: vigor, absorption, strength, tactics, and weapon of choice.
