I also want to know when Link's eyes were ever brown. I mean sure, much of the official art from several games features Link with black pupils, but I don't recall an instance of brown. I attribute two first instances of Link with black pupils - LoZ and AoL - to the generic art design they were going for, which does not appear to pay very much attention to detail.
A Link to the Past
Adventure of Link
The other instances of such - Wind Waker, Four Swords, Minish Cap, Phantom Hourglass, Spirit Tracks - I attribute to the general new design of Link; with the whole Wind Waker look carrying over to other titles. To be honest this design would look odd with blue eyes, and the black pupils work pretty well IMO.
The Wind Waker design that carried on to FS/FSA, MC, PH, ST.
Aside from those instances, Link has been portrayed with blue eyes in the following games: A Link to the Past, Link's Awakening, Ocarina of Time, Majora's Mask, Twilight Princess, and Skyward Sword.
1 ALttP | 2 OoT | 3 SS