After re-watching episode 2, it turns out the honeycomb under the apple tree on the town emblem may simply refer to the name of the apple tree. Regina says to Emma:
“Did you know that the honeycrisp tree is the most hearty and vigorous of all apple trees? It can survive temperatures as low as 40 below and keep growing. It can weather any storm. I have one that I’ve tended to since I was a little girl. And to this day, I’ve yet to taste anything more delicious than the fruit it offers.”
The type of apple tree is called honeycrisp, hence the honey on the emblem. I think that the apple tree is also a metaphor for Regina. When she is speaking about how the tree can weather any storm and freezing temperatures, she is referring to herself. The more I think about the connection between Regina and that apple tree, the more I think her last name, Mills is connected to the Greek word milo for “apple.” Here is a link for the honeycrisp apple: http://en.wikipedia.org/wiki/Honeycrisp
"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