I have actually changed how I do eyes on horses since I initially posted to this thread and rarely use stippling for eyes now. I now mostly use the fiberglass brush (with some re-inking) which gives a softer, more subtle feel to the eye in my opinion. Other times I use very fine lines made with the scalpel (again with re-inking).
Fiberglass brush: "Tassels" - 8"x10"
Much magnified close up of the eye created this way:
And this one with fine lines: "Wisdom" 10"x8"
Much magnified close up of the eye created this way:
However if the eye is a very small part of the board (or on a very small board) I might still use stippling, as it is difficult to control the fiberglass brush in small areas and stippling does give a satisfactory result.