During my Navy flying career I flew through my fair share of thunderstorms (and not because I wanted to). In fact, in my sixteen years in the tactical jet business, three of the Tomcats I was riding around in were hit by lightning, most memorably while climbing out of Wright-Patterson Air Force Base in section where the bolt jumped from our jet to the wingman's. While both jets continued to work normally and we pushed on for NAS Oceana, the strike definitely got the attention of all four of us. When we got on the ground our maintainers pointed out where the bolt had exited our jet, evinced by a charred quarter-sized hole in the trailing edge of the left horizontal stab.
This cool shot was just forwarded to us showing an All Nippon 747 hit while launching out of Osaka. What I can gather from surfing around the Internet is the jet came back around and landed safely.
And here's a quick video of the same strike.