What does Zeniba represent? This is how I interpret the story of Spirited Away:


The bathhouse represents the society. People work with each other towards a common goal. Every night, 8 million gods come to the bathhouse and workers serve them, worship them. In a way they deal with them, do business with them. In Asian cultures, fire, air, earth, water, food, etc. are represented as gods, so bathhouse very accurately represents a working society. The 'spell' breaks if they stop working.
Yubaba is the culture. She manages the bathhouse. She is tyrannical and rules over people by taking there real name and giving them a new name.
Chihiro was given a new name by Yubaba, 'Sen', which means 'one thousand', similar to how a person is given a roll number or employee number in an organisation. That number becomes his new identity.
Haku has forgotten his real name. Similar to Islamic terrorism, he's become a slave to the tyrannical culture. He'll do anything the culture tells him to do.
The baby is the belief system of the society. Yubaba is overly protective of him.


One thing I can't understand is, who is Zeniba, Yubaba's twin sister.


Yubaba and Zeniba are two parts of a whole.
Yubaba keeps baby locked in a room, afraid that he might get sick because of germs. Zeniba turned baby into a mouse so that he might have a little freedom.
Zeniba lives in swamp bottom.
There used to be trains running between bathhouse and swamp bottom in old days, but the return trains from swamp bottom have stopped. Now it's a one-way road towards swamp bottom.
The tickets to swamp bottom Kamaji gave to Chihiro had been with him for 40 years.
'Zeni' has two meanings in Japanese, 'money' and 'ancient'. 'ba' means 'old lady'. The meaning of Zeniba which seems to fit the story is 'ancient old lady.
Yubaba wanted to steal a seal from Zeniba, which was supposedly very precious.


So what does Zeniba represent in this story?
For me, it was old money vs new money. Yubaba keeps rushing to make money, accepts tourists etc. Money became not the means to an end but the end itself. Her bathhouse is modern corporation, Zeniba's house is old school mom and pop store. Chihiro gets her first job in a large corporation, gets treated as disposable, grows up... But it is no way to live, to truly be adult, that is not the true meaning of adulthood. There has to be more to life than money. And it is Zeniba which shows her true grandmotherly kindness and gives her some peace and respite from the story.

In a way, Zeniba is at peace with nature. She takes what she needs from it, but no more than that. Yubaba uses nature to gain money and she only cleans the river god for gold. And Zeniba doesn't do much, maybe because she is retired; in modern world, people don't search for her, her ways are not wanted anymore. Her entrance in the story can be seen as reaction to Yubaba's actions. 

"You and your corporate thinking are not all powerful and all good, Yubaba. I will show you the different way to do things. The old way!" Zeniba says with her actions. And it turns out that there is value in old ways, in traditions long forgotten. That is my interpretation at least. They represent old ways to do business and grow up and new ways to do that and you need to understand both to be a complete person and live in modern society which at the same time has long traditions.

Also, an interesting thought and a way of looking at the story:
Sen didn't search for Zeniba until she has seen naked greed of her coworkers, until she has seen them consumed by it. A lesson can be seen as this: As long as you spend all your time at work, you will not see your parents again. If that is what you truly want, then stop working, visit your grandmother and your parents will return to their senses and see you again.