I'm sure someone will remember what book this was from, but there was a Batstory (official one) somewhere where Gordon had long since moved on and someone, either his kid or partner, was told by Gordon to find his secret files. In those files, which I like to think I remember was something bat-related, it showed that Gordon had known for a long long time that Batman was Bruce Wayne, but choose not to tell.
Dang, someone remember what that was from, because now I want to reread it.