How to make secret doors, walls & floors

There are a couple of ways to make secret passages in your maps.

Method 1: The Simple Method

Go into edit mode and make an ordinary wall that you want to be able to walk through.
Select the part of the wall you want to walk through.
Move to the other side of the wall
right click on the other side.
Hit f3
Go to materials, and select noclip.
And its done. Hit e to exit edit mode, and you should be able to move through the wall. Simple.

This is theoretical - I've never tried it, but I cant see why it wouldn't work.
Make your wall as per usual in edit mode. Now find the texture of the wall you just made (normally located in packages/textures)
Either make a new mapmodel, and animate it, or edit door number 2 in packages/models/doors/doors_02, so that it is totally flat. (For both of these, look at the Adding Models to Sandbox tutorial on the main wiki page, under the Advanced Topics heading)
Make the skin of the mapmodel the texture you located in the first point.
Load the model in the game, load the model into the game.
Delete the cubes behind where you want the door to be.
Position the door in the place where you want it to be, if the size of the door is slightly off the size of the hole, use f and scroll of the size of the hole, until it fits.
Use triggers to determine what opens the door.
- http://sandboxgamemaker.com/platinumartssandboxeditref.html ss useful when doing this.

All done!