Here's a guide for newcomers:
To start playing a puzzle, click it with the mouse. This will cause the text to go from gray to black, and gives the game "focus". Only when the game has focus can you enter letters. If you click outside the game rectangle then the game will lose focus and turn gray again.
Once the game has focus, you can start to guess plain-text letters. To do this, you have to highlight the appropriate encrypted letter, and then press the key of the plain-text letter. The currently selected encrypted letter is the one with the red rectangle over it (like this ). So let's say you think that the encrypted letter 'T' matches the plain-text letter 'S'. Then you would highlight the letter 'T' and press the keyboard key for 'S'. There are two ways to highlight an encrypted letter. First, you can move the mouse to move the red rectangle. Second, you can use the arrow keys to move the red rectangle.
Underneath each puzzle, there is a button that says "Get Answer". Clicking this button will show you the answer to the puzzle, but will not work until at least one day after the puzzle was posted. Also, each puzzle has a link underneath it that allows you to get a PDF version of the puzzle that you can print out and work with a pencil.