It was the starter relay connector on my ninja that was loose.
Put the battery on a trickle charger overnight something like 2A for a good 10 hours
Check the battery with a multimeter and make 100% sure its good.
Im no expert but i believe the clicking is coming from the starter relay and its doing so because the voltage at the starter relay is dropping below it's needed voltage. The reason the voltage drops is due to insufficient current to the starter motor, which could be:
1) Insufficient battery charge
2) Mechanically-bound starter motor
3) loose or corroded connections in the starter circuit
look at the troubleshooting guide here:
I believe the starter relay is under the seat next to the battery near the junction box.
The starter motor on the other hand is alot harder to get to.
Download the manual if you haven't done so already.
hondatech.info: Honda service manuals