True his eyes are not the typical. they're not even like the eyes of any of the other characters in Death Note. They're lifeless eyes. There is no light in them, they look like water color circles.
The rest of the characters have a black pupil, and depth in their eyes. You can see the play of light, and color, in their eyes.
His eyes (L's) have nothing to them. I would have to agree with you they are creepy. Which gives him a somewhat creepy look overall.
However, "L" is still my favorite character in Death Note, he's great!