This game can be played here
I wrote this late 2013 and looking back there is quite a bit I would change.
A few of the issues I noticed while glancing the code:
The program at times queries the DOM for data and then writes back to it (namely score and timer). It would be much better to move all game state to a single object and then use that within any function to render the view.
It seems like I originally built reasonably small functions, but they reference and mutate outside objects constantly. It's up to the programmer to keep in mind what all the moving pieces are. It would be interesting to transition this to a more functional style that receives the current game state and computes the next game state.
The mole's movement is being handled by CSS Animations. Since each level has moles that behave differently, these CSS rules are being changed by using JS to reaching into the DOM and edit the stylesheets. It may have been easier in the end to just use JS to handle the animations directly by setting properties on the moles. It would also have the benefit of pulling the mole's position into the game state data and consolidating more of the game's behavior in a single place. However, part of the learning exercise for me at the time was using CSS animations instead.