I'm not sure of the ship names for all the pairings, but here's what I can think of . . .

Swan Queen (Regina/Emma)
Outlaw Queen (Robin/Regina)
Fairy Queen (Tinker Bell/Regina)
Stable Queen (Daniel/Regina)
Rumpelstiltskin/Regina
Snow White/Regina
Charming/Regina
Mad Queen (Hatter/Regina)
Regina/Red
Captain Swan (Hook/Emma)
Swanfire (Baelfire/Emma)
August/Emma
Red/Emma
Jefferson/Emma
Rumpelstiltskin/Emma
Mary Margaret/Emma
Red Snow (Snow/Red)
Charming/Snow
RumBelle (Rumpelstiltskin/Belle)
Rumpelstiltskin/Cora
Rumpelstiltskin/Zelena
Sleeping Warrior (Mulan/Aurora)
Phillip/Aurora
Robin/Mulan
Robin/Marian
Jiminy/Red
Dr. Whale/Red

I know I'm missing some more, but my brain's drawing a blank now. Of course, if you're going to be including Wonderland, there's Will/Anastasia, Cyrus/Alice, Will/Alice, Anastasia/Alice, and the White Rabbit/his wife (forget her name).