Mulan gives Emma poppy dust to knock the giant out. This alludes to the field of poppies the Wicked Witch of the West uses in The Wizard of Oz (1939) to knock out Dorothy and her companions.
Neal Cassady was a member of what is commonly referred to as the 1950s Beat Generation. He is known to be an inspiration to writers Allen Ginsberg and Jack Kerouac as well as later generation, Ken Kesey, among others. Like his character sharing his name here, he was known for his charm and for stealing cars.
In the convenience store that Emma and Neal are stealing from, there is a leather keychain hanging by the cashier with the name Henry prominently displayed.
When Hook dresses Emma's wound when they reach the top of the beanstalk, he seductively ties his scarf around it with his teeth. This was not scripted, but improvised by Colin O'Donoghue. Jennifer Morrison had no idea it was coming.
The object/animal/person in this episode is a growing beanstalk.