His eyes are hazel. The dominant colours in hazel eyes are brown and green, and they do appear to change colour. The inner part can be light brown, with amber to dark green at the outer edge, or vice versa. Jared's eyes are just gorgeous, no matter which colour they appear. :))
My theory is that he is so amazingly gorgeous and god-like, that his eyes magically change color from episode to episode. I mean, in one they look brown, then hazel, then green, then a really dark brown, almost black, then back up to blue-green! What can I say? The man is magic. Magically delicious! (teehee)
All of the answers are correct, his eyes change often. I'd say the majority of the time his eyes are hazel, but at different times they are also blue/green, blue/gray, gray/green. If I had to choose 2, I'd say his eyes are hazel or blue/green most of the time.