In Yu-Gi-Oh! any character that's under the control of the Sennan/Millennium Rod has no/loses their pupils,here's a picture of Anzu-chan/ "Tea" in the english dub under the control of the Rod..if that counts.
Everybody seems to have strange eyes in Amnesia. Not sure what his name is, but it looks to be the guy with the कुदाल, कुदाल से खोदना shaped tear tattoo thing.