The mini golf at Wanneroo Botanic Gardens, in Drovers Place corner of Wanneroo Rd, has to be not only the best challenging course on offer but set in the prettiest surroundings as well. The owners did a fantastic job of creating a lush tropical feel to the previous barren site. There is a great cafe - Leap Frogs, on site as well.
Murdoch Pines is a great place to play Mini-Golf. Their prices are quite cheap compared to other Mini-Golf places. They also have very challenging holes to improve your game and a golf course right next door.