City of Amnesia

At the end of Big O, most of the people in Paradigm were revealed to be cloned from real people before the event 40 years prior.  However, was that the reason they can't remember anything, or was it because their memories were somehow stolen from them?

I'm not sure that it was revealed that most of the people were tomatoes. One of the biggest problems for the inhabitants that is you can't remember much from when you are young, so you may not know how old you are. Therefore you can't determine what being you are. Anyway, it was said in the show that even the most successful tomatoes, ones that weren't cast into the wastelands, could remember the event, but could not remember anything before it and were killed once they became aware of that fact. Memories were taken from anyone who lived through the event isn't necessarily true. Roger hints at the fact that he originally had memories, but gave them up willingly as did Gordon Rosewater. The android senator had some before he was killed by Alan Gabriel, so the nature and outcome of the event isn't fully known either.

The more I think about this the more I am reminded how the Face Dancers calling themselves "Daniel & Marty" in Herbert's Chapterhouse Dune created a hallucinatory overlay over their world which mimics a country cottage on rural Earth when in fact they were located in no such place. The tomatoes and the tomato farm (and perhaps all of Paradigm City) could be just a way for Gordon Rosewater to "interpret" the complexities of the world he ran (or created). If things, or people, became too complex as they were perhaps it was easier to just re-vision them as tomatoes growing on a farm.

As I can recall, that wasn't revealed at all.

Nothing was "revealed" so much as tons of things were splashed and thrown about haphazardly because they needed to finish and had thought they were getting another season to do so until the last 2 or 3 episodes.

Well, I rewatched Big-O I and Big-O II again. The last few episodes revealed very little and made the story a bit more confusing.  Before Big-Venus reset everything, Gordon Rosewater mentioned that the book he wrote (The Metropolis) and everything in it were all made up.  But the interesting thing is is that he was involved in creating people with "certain memories" or beliefs, you would call it those instead.  Anyway, that's about the only few things that were revealed, and the supposed "event 40 years ago" is always considered when the people of Paradigm can't recall what happened before 40 years ago.

In a way, Big-O is like Plato's parable about the Cave.  Or was it Socrates?  Anyway, the cave was where people inhabit, and the shadows from the fire in the cave is nothing more than an illusion that controls the people.  The same sorta can be said about Paradigm City with the Memories and Alex Goldwater. I'll try to explain more later. 

Uh its written by plato but it is Socrates talking to a guy called Glacon or something?

I recommend watching a movie called Dark City. It's not that great but it does center around a certain urban with absolutely nothing else but the city itself existing to the and the main character slowly gains reality warping powers and at the end (spoiler!)  rewrites the city how he sees fit from fabricated memories of his childhood. The 24 guy is in it if you want to see Jack Bauer not kick any ass at all.