The quest for Shadow of the Colossus' last big secret (2013)
eurogamer.net
eurogamer.net
http://goldeneye.wikia.com/wiki/Citadel
It wasn't really an intended secret. It sounds like to make it accessible, a player had to hack it in, and to make it playable, another player had to contribute clipping information.
Sometimes the journey is more important than the destination.
Other times they are really nicely fleshed out, but locked away behind flimsy "gates", and really were intended to go into the full game, but had to be abandoned at the very last minute.
And then there's the cinematic areas that are made for show, implemented as they were intended, which never included being accessible to players.
What's really the most rewarding thing about this is that you, as a player, as an explorer, get to puzzle things out; you almost get to write the narrative yourself.
It also helps that there really were some great hidden bits. The game is riddled with wonderfully hidden special spots. (If I remember correctly, it's a bad idea to eat the fruit in the garden at the top of the temple.)
When Myst Online: Uru Live got its second wind, a similar air followed the gameplay. Everything could be a puzzle or a plot with each new update. I always felt the Cyan developers knew they had to make puzzles that not only stumped a player, but a whole community of fans. I had enormous amounts of fun searching for and - in the end inventing - puzzles there. To this day I like to think Jalak was totally a puzzle, and not just a surprisingly involved gizmo.