When Henry came, Emma thought the best thing for Henry would be for him to go back to regina–twice she did so, all for Henry. It is only when she notices how controlling and possessive she is, as well as how miserable Henry is, that she decides to stay in Storybrooke. And even then, she was still planning on leaving–Regina purposesly tricked Henry into listening to the conversation between her and Emma about how the latter thought the curse was crazy.
Yes Regina loves Henry, but many of her actions have resulted in hurting him, and Emma could see that. That was one of the reasons why she stayed.
And I think she also stayed because of Mary Margaret–the latter helped her to find the courage to be there for Emma, she bailed Emma out of jail, and she provided a home for her, asking for nothing in return. 🙂 These acts of kindess, of being wanted, were what inspired her to stay, also.
And then when Graham died, and when Henry gave up hope and claimed that good never wins, Emma stayed to show him that good can win. She wanted to show him that and also to be his hero 🙂