One theory that we find convincing is that Cora is the Queen of Hearts over in Wonderland. And a recent statement from the showrunners leaves us thinking it's likely to be true.
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Update! 11/28: On of the most convincing pieces of evidence for us is that the Season 2 winter finale (Season 2, Episode 9) is called "Queen of Hearts." According to the press release about the episode, Cora just so happens to play a major part on the present-timeline parts of the episode, while the flashback involves Captain Hook (Colin O’Donoghue) seeking out the Queen of Hearts. Captain Hook ... who is now teamed up with Cora. Coincidence? We're thinking not.
Even more convincing is that showrunner Edward Kitsis told TV Guide that the Queen of Hearts very well could be someone we've already met, and we'll definitely find out who she is in "Queen of Hearts." Why would they focus energy on a new character in the winter finale?
Cora did go "through the looking glass": In "We Are Both" Rumplestiltskin (Robert Carlyle) encourages Regina to push Cora through a mirror portal to what he calls "a specific, annoying little world." Meanwhile, in Jefferson's (Sebastian Stan) hall of portal doors to other worlds, which we saw in Season 1, Episode 17: "Hat Trick," Wonderland was through a mirror. This also connects to the title of the sequel to Alice in Wonderland, which is called Through the Looking-Glass, and What Alice Found There. It's very possible Regina sent Cora to Wonderland when she pushed her into that mirror.
Cora is power hungry: If Cora did end up in Wonderland, it's easy to imagine that her reaction would be to grab for as much power as possible.
Cora and hearts: Cora is very connected to hearts already. She rips them out of people, and, as we saw in "We Are Both," her book of spells has a heart on the front.
The Queen of Hearts has it out for Regina: We don't know what the history is between Regina and the Queen of Hearts, but it's obvious they have a connection. The Queen of Hearts kidnapped Regina's father and kept him in a box in Wonderland (as we saw in "Hat Trick"), and she freaked out when Jefferson referred to Regina as "Queen." While their enmity could be connected to something else — it's easy to see why either woman would dislike the other, since they are both power hungry and evil — it could also stem from the Queen of Hearts being Cora.