Right at the start, when you go down the elevator, there are two bookcases. Headbutt the wooden thingy between them. One of the bookshelves slide away.

Right next to the silver-key door is this strange thing. There must have been a interior designer around. Jump over the spikes and hit the red pole. A secret area opens in the next room, the one with the auto-shooter.

When you take the silver key, you look down on a yeechy-looking altar. Behind it is three candles, the middle one is dark. Shoot it. The front of the altar opens, revealing a button. Shoot it, one of the stained glass windows opens. Jump down and get goodie.

You reach a bright stained glass window and a button at the end of a hallway. Shoot the window. This triggers a lift, that takes you up to the last secret.