Grimrock

There's a dagger behind the iron door at level 3. The door is opened form the "Good students area" where there is a row of altars.

Before the altar for the god of thunder. Directly when you come up the stairs, there is a corridor, with a portcullis and a pull chain. In that corridor there is a secret button. Push that. Then go past the altar and down that corridor. A secret door should have opened. In the new area there are three alcoves. Fill them and one more secret door will open. Inside there is a teleporter that will take you to the catacombs.

The gems are in two student quarters. Galten and Brimp.
In Glaten's quarter, there is a secret button behind the wall tapestry, then you need to break some furniture to get to the room that opens.
In Brimp's quarter, you need to put something in the bookshelf.