Minecraft wiki entry for Locked_chest, associated text: Steve Co. Supply Crate is a reference to the Mann Co. Supply Crate[3] from Team Fortress 2, where a key must be purchased for $2.49 in the in-game shop called Mann Co. Store in order to open the crate.[4]
This may have been what Notch was talking about in his Twitter post about a "silly secret project".[5]
At the time of the locked chest being added into Minecraft, it looked identical to a normal chest. However, after Beta 1.8, when the chest model was updated to be smaller than a full block, the locked chest, a deprecated block at that point, remained with the old model, and as such became larger than an ordinary chest.
Unlike normal chests, locked chest luminates the world with a light level of 15. This was probably done to allow players to differentiate itself with normal chests.