You cannot enter the three secret rooms on your first play-through of the game. The opportunity to earn this will come in the second play-through of the game, having been given the Golden Key for completing the game the first time. The Golden Key will unlock all three secret rooms.
The three Golden Key rooms are located in these areas:
From the starting EdgeWood screen, go 1 right. See that gate that wasn't open-able in the first playthrough? Well, now you have the key! Walk up to it and click on it to open the game, and head in.
Remember the very conspicuous door you couldn't enter last time in Hangley Pass, right after the stone that drops after shooting out its brace? Its on the screen with the broken bridge, right before the house with the re-spawning demon. To get there from the starting Hangley Pass screen, go 1 right, 1 upper right, 2 right, 1 upper left (using the bouncing mushroom to get to the top left platform -- you'll need George to dig up the mushroom), 1 upper right. 2 right. With the golden key, you can now enter this door.
The Sack Chute
The first screen of the Sack Chute has the secret room door right on it, how convenient!