I have a few questions regarding the Break Enchantment spell:
1) Can Break Enchantment be used to reverse petrification from a Gorgon's breath or Medusa's gaze? On the one hand, nothing in the spell specifies that it only works on spells only. On the other hand, it assumes a caster level for the effect to be undone.
-No, unfortunately, the Break Enchantment spell refers to spells and effects caused by spell-like abilities. A medusa's gaze and a gorgon's breath are Supernatural abilities, and the effects are only reversable with a Stone to Flesh spell, Wish, Miracle or the like.
2) If Break Enchantment can be used to reverse a non-spell-based enchantment, transmutation, or curse, how do you set the DC for the caster level check (normally 11 + caster level of the targeted effect) if there is no caster level given for that effect?
-You can't.
3) Flesh to Stone is a 6th-level spell that has an instantaneous duration and cannot be dispelled (the Dispel Magic description specifies both instantaneous duration spells and petrification as effects on which it will not work). In the PHB, Break Enchantment specifically mentions Flesh to Stone as a spell it can reverse. It also says that if a spell cannot be dispelled with Dispel Magic, then Break Enchantment can only reverse it if it is a spell of 5th-level or less. Taken together, this does not make sense. Either Flesh to Stone cannot be affected by Break Enchantment, or
Break Enchantment can affect at least that one particular 6th-level spell. I notice that the SRD, unlike the PHB, does NOT mention Flesh to Stone as an example spell that can be undone with Break Enchantment in the latter's description.
-At this point, unless we release errata to the contrary, I would say that Break Enchantment cannot reverse a spell higher than 5th-level, with Flesh to Stone being the only exception.