In a certain druid stronghold quest, the Spirit of the Grove asks you to kill a troll shaman. When you do so, s/he rewards you with a magical club, the Root of the Problem. (+1, +1 acid damage, +3 vs. unnatural creatures) The question is, which creatures are considered "unnatural" and which aren't?

I think 'unnatural' means for example magically created (think golems) and undead creatures. (I'm not sure though)

Monsters, undead and giant humanoids.

Examples:
golems, ogres, genies, etc - giant humanoids

otyughs, salamanders, big spiders, beholders, etc - monsters

undead - undead :p