Just the 2 side doors in Samuel's lair are available; the rest is just background.
If you leave the lair, one of the keys from a side room will open a door a bit to the west, just past the corridor, into a room with a set of stairs that leads to the end of the act (one-way trip).
A key from the other side room opens the blacksmith's door in the far north east of the citadel, where you can get a hint for something to do there...
<span class='standouttext'>Spoiler : </span><span class='spoiler'>There was a book near the start of the game describing how to make gunpowder. If you combine coal (Furgus' room), salt (citadel kitchen) and then sulphur (gay medic's room) to make a bomb, you can drop it onto the forge to flood the citadel and move to the next act (unlike leaving by the stairs, this gives experience points).</span> (highlight the text to read)