Are you talking about the noodles (to eat) or Mr. Noodle? As the actor who Mr. Noodle from Sesame Street plays the scoutmaster in the begninning
http://www.imdb.com/board/20410347/

Use your noodle!!!!

might be some kind of reference to the brain.

They're freeze dried, then you make them instantly.

I think Joel got it pretty accurate, and didn't even think of the Maruchan thing.
I think while they were under control they were just fed cheap-enough food to keep them alive while being brainwashed. After being released they kept on eating the only food they ate during brainwashed as a likely unintended side effect.
Sidenote - adding tomato to cheap Ramen noodles is delicious. I call adding celery, onions, carrots, etc "Adult Ramen" - a much healthier experience and still less than $2 for the whole meal

Well, there could be a couple of reasons why this is included in the film.
First though, the brand of noodles is "Cup Noodles" in the film. The packaging seems designed to mimic that of Maruchan noodles, a real-life brand of instant noodles. "Maruchan" can either be a witting or unwitting reference to "Manchurian." Irregardless, the film shows that the consumption of noodles is a part of Shaw and Marco's programmed behavior. You will recall seeing Marco eating instant noodles while his fellow soldiers were being tortured. Thus, we must assume that the noodles factor in to the construct in which Shaw and Marco inhabit.
I think the noodles represent a cognitive trojan horse which allows the artificial behavioral construct created by Noyle to remain intact withing Shaw's and Marco's subconscious while they go about their daily lives. It also acts as an unconscious association, causing them to never be free of the trauma of the torture they endured, thus keeping the reprogramming potent in their mind, though never revealing the true purpose of its intent.

Product placement. It's common in movies.