What I've been finding lately is that, 9 times out of 10, lightning hits actually come through the phone line, and not the power, and I have successfully been using the following method to repair affected motherboards.
I covered the area around the Ethernet controller with Aluminium foil to shield it, with a small hole in it above the Ethernet controller. I then proceeded to heat up the exposed Ethernet controller IC with a hot air gun for a good minute or so, and then I was able pry it off with a flat screwdriver, and clean up any excess solder from where the IC once was with my soldering iron and de-soldering braid.
So, the only problem is that the Ethernet controller IC shorts as a result of the spike, and prevents the board from starting. The three boards I've done it to all seem to work fine with the Ethernet controller IC missing (minus the onboard Ethernet, of course)
My most recent save with this method is a Gigabyte GA-Z77M-D3H-MVP (the other two I've done it to are a GA-G41M-ES2L and a Dell DH57M02). I'm considering getting a 3570K or 3770K CPU and updating my main rig with it. Not bad for a freebie motherboard, if I do say so myself