Clicker training is a form of positive reinforcement, so rewarding wanted behaviour using kind methods.
The clicker is used when a behaviour is being rewarded, so for example you want your bunny to come to you when called, when the bunny comes (or goes in the right direction if you are using shaping) you click the clicker and give a food treat. The clicker must become a conditioned reinforcer first by pairing it up with food, so the bunny learns it is the click that is the reward not just the food (which is the primary reinforcer). It associates the click, with the arrival of food, and the clicker soon becomes enough of a reinforcer for animals to work for it.
It's basically a way of training and can be used in all animals and is based on how an animal learns. There are lots of great books out there, especially ones by Karen Pryor as she introduced it to the dog world (originally she clicker trained dolphins). Sorry if the above was a bit technical, if you don't get it I'll try put it into plainer English!!!
If you want anymore info just PM me as I'm really into clicker training, well dogs and all animal training in general really!!
Nicola