As of June 2014 (with the last update coming from Map Pack 2 in October of 2012), there are eight secret achievements according to the Steam achievements page.
Voyage au centre de la Terre Edit
Obtained by jumping onto a pipe beneath the maze on Mine, and following the path until you enter a portal to a hidden area.
The name of the achievement is French for "Journey to the center of the Earth."
The Plot Thickens Edit
On Bridge, walk across the platform nearest the core. Look down through the grate and you'll see a lower platform which you must fall onto by simply dropping and holding the directional key required to hit the platform below. Now walk into the hidden room.
The Monument Edit
On Arc, jump from the upper platform to one of the metal scaffolding rails, then follow the scaffolding that leads under the bridge until you find the rings, jump from ring to ring until you find the broken tiles and then finally over the tiles to the monument.
Keep quiet Edit
On Glade, you'll first need to reach wave 14.
Now, during the build phase, make your way to the right side of the field (left side on overview map) and jump down one of the square holes. If the prerequisite has been fulfilled a hatch here should open up (slowly). Jumping down will teleport you to a secret area. Once you've reached the end (requires some jumping), the achievement will be unlocked.
On the map Facility, make your way through until you reach wave 20.
At this point during the build phase head to the core and face the enemies spawn. From here go left to the spire-like tower and head up the stairs. Jump down to the end of the tunnel and jump at the door. It will open and once you walk inside you will unlock the achievement.
A Future FriendEdit
On Yogscave, there is a stash of cakes to the left of the core. If you go forward towards a machine, you can find a person using a computer. Standing near him will unlock the achievement.
On Chasm, there is a ledge with a root that you can jump onto. If you follow the root upwards, you will find an open area with a grill and an icicle above it. You have to shoot the lid off of the grill and then shoot the icicle to make it fall onto the grill to unlock this achievement.
Strawberry Fields ForeverEdit
On Invasion, there is a small gray block on top of a beam. You have to shoot the block off the beam and then try to shoot the block towards a strawberry that is in the