Are there any official rules for damage done by non-magical lightning?
Say one of your player's characters is standing on a mountain during a thunderstorm in wet copper armor swinging a sword around shouting profanities and insults about the gods, if she gets hit by lightning not made by a "call lightning" spell or the like, how much damage would it do? Is this just left to GM fiat?
Here you go:
Thunderstorm: In addition to wind and precipitation (usually rain, but sometimes also hail), thunderstorms are accompanied by lightning that can pose a hazard to characters without proper shelter (especially those in metal armor). As a rule of thumb, assume one bolt per minute for a 1-hour period at the center of the storm. Each bolt causes between 4d8 and 10d8 points of electricity damage. One in 10 thunderstorms is accompanied by a tornado.
In short, GM fiat. However, I would compare the danger to similar hazards or traps. For example, a Cave-In (CR8) does 8d6 (avg 28) damage with a Reflex DC of 15 for half. It also has a bury component that can kill over time although that really isn't a major issue for most adventuring parties.
A lightning storm with 7d8 damage and a reflex save of 15 should be close to a similar CR but maybe a bit lower due to no bury component. I would call it a CR 6 or 7. Also reduce the CR if the bolt only strikes one target at a time.
Alternately, if we compared the CR to a trap then we get:
+1CR (*2 if multiple targets) per 10pts average damage
-1CR for a Reflex DC15 (+0CR for DC20)
-1 CR for the Perception check (lightning storm should be obvious)
Effectively +3 for the Disable Device check (impossible to disarm).
+1 for Automatic Reset (1/minute)
So: at 7d8 we get: +3 (*2?) damage -1save -1perception +3disarm +1 reset = CR5 or CR8 (if multiple targets).
So, similar to the Cave-In if multiple targets.
Note: I believe Pathfinder CRs (and the Cave-In CR) are too high for traps so I typically treat all trap CRs with a grain of salt. I often drop them 1-2 to represent the actual difficulty for many people.