I've never done it but this would be what I'd try -
Make the picture Black and white. SAVE it - and if you have photoshop ...zoom in on the picture - take the paint tool - choose your color and very carefully & fill in the iris....go slowly cause doing that kind of work is tricky - also if you know how - i would try the smudge tool to blend in the color a bit.
you can also do little things like put a white dot on each eye to make them more real looking - when I fix peoples photos I re-create eyes ....adding that white dot will take away the "Stepford Dog eyes" that most red eye tools do....
if you don't have photoshop - there's a program called GIMP I think put out by google - it's called the FREE photoshop - you can get it here - Picasa
http://www.get-picasa.com/?r=mp