I had some conversation with an electrician about this once.
As I recall, his recomendation was a surge protector that plugs into the circuit breaker panel like a breaker. I know Square D makes them and I believe they're available for other brand boxes as well.
The suppression is limited, the ones we sold at Lowes were only rated to 20,000 volts, lightning can be a lot more than that. But 20,000 volts will squash any garden variety surge that comes down the line. To work correctly, they need to be plugged into the first position on the panel.
Some building codes are starting to require the plug ins.
None of the plug ins will protect from EMP, that's another issue altogether.
Hope this helps XT.