Shattered Kingdoms

Okay, so say NPC A casts Flamestrike on my horse and my character wears magic resist. Does the spell run a check against each individual target or just the horse's MR / MP?

Each individual person. That is why mass healing magic (refresh, mass heal) will sometimes fail on certain people.

If they land a succesful flamestrike on another member and you succeed your MR check, you will simply get the white message - same with cone of cold.

If they try to flamestrike you, and you MR, I'm quite sure that it never gets around to check whether your grouped and the spell 'fizzles' - not sure about the latter one, though.