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Solving a sonar-based Glyph puzzle reveals a hidden message quoting a Hopi prophecy warning of "a container of ashes" thrown from the sky that would burn the land and boil the ocean, an omen tying into the series' looming solar-flare apocalypse.
Visit the Sistine Chapel in-game and Michelangelo's famous ceiling fresco is nowhere to be seen, not a graphical shortcut, but historical accuracy, since the game is set in 1499, several years before Michelangelo began that work.
In the Strangers and Freaks mission 'The Last One', Franklin meets a hunter who claims he's been chasing a Sasquatch for nine years. That's a deliberate reference to GTA: San Andreas, released exactly nine years before GTA V, where rumours of a Bigfoot sighting first took hold of the community.
In the beta release of Halo 3 multiplayer mode, if you angle the camera just right while on a mongoose, you can clip through the Spartan's helmet and it'll show a face underneath. Which is the image of Marcus Lehto, Bungie's creative director from 1997 to 2012.
