Thank you for your question regarding lightning protection and ferrite chokes, it is our pleasure to help.
Ferrite chokes are used to filter common-mode noise and interference on data lines such as CAT5 Ethernet. Ferrites operate on low-power high-frequency signals that are coupled onto the line from neighboring cables or wireless transmissions. They are not designed to protect from high-power surges such as lightning or short-circuit events. In high-power surges, ferrite chokes become saturated and become ineffective as filters.
For lightning protection, you need a transient voltage surge suppressor (TVSS) for Ethernet, such as those offered by PolyPhaser and Transtector.
Of course, the best way to protect the sensitive electronic equipment tied to your Cat5 cable, is to make sure that the difference in potential between the two pieces of equipment is very low, something less than 0.1 ohms. If there is no difference in potential, than no harmful voltages can form in the first place. Good bonding between these points, along with a low-impedance electrode, will be one of the best methods of protection.
We hope you find this information useful. If you should have any further questions, please do not hesitate to contact us again.
The Engineering Team at E&S Earthing Solutions
Photo credit: http://www.flickr.com/photos/picofarad-org/2132207664/sizes/l/in/photostream/