The logical guess – Assuming Dragon = reptile (I hope no body will argue with that ^ - ^), hence they have yellow-green eyes.
The scientific guess - Dragons, according to text (I don’t think this is reliable….well I will still publish just for your viewing ^ - ^) are resistant to heavy metal-poisoning and live in environments where heavy-metal poisoning is possible. So depending on the type of metals involved a dragon's eye can be a wide range of colors: Cobalt - sky blue , Iron – orange, Chromium – orange, Silver – black and Gold - bright purple.
The artistic guess - All evil dragons' eyes are having black pupil, & red for the rest. Whereas good dragons have some variations from the normal (variations? …. meaning any color also can??!...). The normal eye coloring for a good dragon is to have black pupils and crystal-blue for the rest of the eye.
You can refer to following link for some impressive dragon eye painting: http://fineartamerica.com/art/paintings/dragon+eye/all
Anyway following are some eye painted up for the prototype for your viewing…. It may not mean much process, but at least it is moving ^ - ^
