After having the car sit for a few days when firing it up now it's running on 3 cylinders.
 
It's a bigport 4AGE running Megasquirt. I put the timing light on the ignition leads and cylinder 3 didn't register anything. I swapped some leads around but it was always cylinder 3.
 
When checking the main lead from the coil it's got an un-even frequency on the timing light. I'm not sure if that's an issue or not?

Given the recent storms in SA, maybe water got where the plugs are and hence causing issues. Try drying them out with some WD40.

After doing what Dylmrt said, pull the plug out and check that it has not cracked or the electrode has no worn away. If that's not your problem, check the cylinder 3 post on the dizzy cap to make sure it doesn't have corrosion or hasn't worn away.

Problem solved! Swapped places on two spark plugs and the problem moved with the plug. Went and picked up 4 new plugs (was about time anyway) and now Im back in 4 cylinder land again. Thanks for the help guys!