Punch Through applies to enemies and allies only, but not surfaces of any kind, e.g. it cannot pass through a Shield Lancer's shield (possible bug due to conflict with bouncing mechanism).
Update 13 gave Power Throw the ability to create explosions when hitting an object on its last bounce. This explosion will damage both enemies and yourself if you're near enough.
Explosion damage scales with Physical Damage and Elemental Damage (For damage outputs against specific enemies look here: Damage.)
A maxed out Quick Return now synergizes well with Power Throw by creating explosions on the first object hit, since the throwing weapon returns to its owner soon after, thus counting as the last bounce.