While I didn't like the game supermuch, the Hook Horror fight in IWDII was fun.  And I loved Dragon's Eye in IWDI. 
  
For future games, I'd like to see someone tackle the idea that the only way to defeat a giant monster is to invade its body, thus the tunnels become various parts of the body where you fight monster parasites while trying to get to the organ to defeat the creature.  Imagine fighting a monster that IS the tunnel!