@ mia: On the topic of “magic” well water, I agree. You could see the wheels turning in Emma’s head when she somewhat rhetorically asked what other explanation there could be. She clearly left out the drink and conversation she’d had with August. Probably, due to her skeptical side, she doesn’t want Henry jumping to conclusions, even though her disbelief may be starting to wain a bit. I think August fed her the water line to start Emma down the road of believing in even the possibility of magic.
On the topic of town emblems, apple trees, and bee hives (which is almost deserving of an entirely new topic thread), in episode 5, That Still Small Voice, Regina makes an allusion to honeycomb.
Regina: People of Storybrooke, don’t be alarmed. We’ve always known that this area was honeycombed with old mining tunnels. But, fear not, I’m going to undertake a project to make this area safe, to rehabilitate it into city use. We will bulldoze it, collapse it, pave it.
It may simply be an insignificant reference. Yet, it’s still very interesting that she uses the word “honeycombed” in reference to the mines, which run beneath SB. The mines also contain the remains of Snow White’s glass coffin. Perhaps they represent a link between worlds?
"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy