While playing Glory of Heracles for the DS, I named the hero Icarus because of the reference to Pit from the Kid Icarus games really early in? the game. Turns out naming him Icarus in this game is 100% accurate given the ending and his mythology. That means that for anyone who's played Kid Icarus or Super Smash Bros. Brawl before playing this game, naming him Icarus is not coincidental whatsoever. Nice job there.
For big time coincidence points, Icarus was Hercules' sidekick in the animated series based on the Disney Hercules movie. I named my character Icarus because of THIS, and still had it end up correct.
This troper picked that name because the name I originally picked didn't end in an 's' and it was the only one I could think of... the only reason the 's' thing mattered to me was because most everyone else's name ended with an 's'.
In the DS game, the final boss has a very One-Winged Angel appearance. The scenario writer, Kazushige Nojima, who worked on the Go H series in the past, also worked on Final Fantasy 7, 8, and Kingdom Hearts. He noted in interviews that he wanted a very old-school kind of story for Go H 5, and the series itself is quite classic in nature. Essentially, he's killing off all of that stuff he had rather mixed feelings for from Square in the form of the characters. This may just be WMG, but it's still food for thought.
A less tinfoil hat example again involves the Take That. If that reference wasn't intentional, given the story context and ending, then that was one serious case of chance working in the right way to foreshadow the hero's identity.