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 13.0 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 2.0).
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.
Update 17.0 also gave Power Throw the added effect for every enemy hit projectile speed is increased. Calculations needed.
Cannot pass through Fusion MOA's Osprey Attack Drone.
Despite seeming to have only 0.6 at max rank, at rank 0 it can go through several Grineer marines and corpus crewmen. It's possible that melee punch-through may be calculated differently than firearm punch-through.