The first one that comes to my mind was Soyuz TMA-22 that launched in blizzard conditions.http://en.wikipedia.org/wiki/Soyuz_TMA-22#Launch
Apollo 12's lightning strike could have resulted in a LOC/LOM scenario. They just did not know enough about triboelectrification.Worst weather (in hindsight) has to be at The Cape in January 28th 1986.