I've just finished watching Episode 12 of Season 1 of Once Upon a Time. As stated by Henry at the beginning of the series, everyone's memories have been erased, including the Mayor's. However, the Mayor is clearly aware that she is the Evil Queen after taking the Huntsman's heart from its box and crushing it.
Later on though, she begs Mr. Gold to tell her his real name, even though it is shown that she knew his name when she was the Evil Queen. Does this mean that she does know the truth, but some of her memories are hazy as opposed to fully erased like everyone else?