I see regularly that schools use Puzzel.org and that is awesome! A feature that will stimulate this use, is the option of having automatic answer checking enabled/disabled.
The answer checking makes sure that every entered answer within the puzzle is being checked against the actual valid answer. This happens via an encrypted route though, so no one will have access to the real answer. When the answer turns out to be false, the colors stay neutral as visual feedback.
In combination with the user-friendly use of Backspace, Tab and the Arrow Keys, it is very easy to undo wrong answers and to jump to the next question.
Answers plus end solution
Besides that, there is a nice feature with which you can connect a final solution to the puzzle, when someone has deciphered all of the answers containing 'hint squares'. This ultimate goal of the puzzle gives a little extra dimension and makes it usable for prize questions.
To be able to use Puzzel.org online, for schools, it is necessary to block any kind of spying on the real answers, even for the smart and technically adept children :). To facilitate this, Puzzel.org saves the answers encrypted. When a puzzle player checks the answer, it runs the same encryption and checks if the encryptions match.
Disabling answer control
As a premium feature, there is the option to disable answer control as well. This will allow teachers to manually check and grade a puzzle based on the filled in answers.
It is also a bit more difficult for the students this way, since you do not know if your filled in answer is valid or not.