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A tour of the Ben & Jerry's factory in Waterbury, Vt., includes a stop at the "Flavor Graveyard," where ice cream combinations that didn't make the cut are put to rest under the shade of big trees.

One recently deceased flavor has yet to be memorialized there: Coffee Heath Bar Crunch, one of the company's best-sellers. Ben & Jerry's CEO Jostein Solheim says the company had to remove the key ingredient, Heath bars made by Hershey, and rework the flavor. Its replacement is called Coffee Toffee Bar Crunch. (Some fans have blasted the company in online forums, claiming it doesn't taste as good.)

The reason for the change? Hershey makes Heath bars with genetically engineered ingredients, and Ben & Jerry's has made a pledge to remove all GMO ingredients from its ice cream.

The company has taken a vocal stand in recent years in support of states looking at legislation that would require manufacturers to disclose food that is made with genetic engineering. And Vermont recently passed a law that will require labeling starting in 2015. Ben & Jerry's co-founder Jerry Greenfield recently launched a campaign to help fill the coffers of Vermont's crowd-sourced defense fund set up to combat lawsuits over its labeling law.

The news that Ben & Jerry's is taking a stand on a controversial issue is no surprise; it's part of the company's calling card. But some other mainstream companies are carefully and much more quietly calibrating their non-GMO strategies.

General Mills' original plain Cheerios are now GMO-free, but the only announcement was in a company blog post in January. And you won't see any label on the box highlighting the change. Grape Nuts, another cereal aisle staple, made by Post, is also non-GMO. And Target has about 80 of its own brand items certified GMO-free.

Megan Westgate runs the Non-GMO Project, which acts as an independent third-party verifier of GMO-free products, including Target's. She says her organization knows about "a lot of exciting cool things that are happening that for whatever strategic reasons get kept pretty quiet."

The Non-GMO Project has certified more than 20,000 products since it launched in 2007, and Westgate says this is one of the fastest growing sectors of the natural food industry, representing $6 billion in annual sales. But just because they're testing the water doesn't mean most mainstream companies are ready to start publicizing their changes.

Nathan Hendricks, an agricultural economist at Kansas State University, says big food producers are trying to gauge what direction consumers are headed in. "Ultimately," he says, "these big companies aren't just friends with Monsanto or something. They want to make a profit, and they want to be able to do what's going to make them money." So they'd better have a product line in the works if consumer sentiment starts to shift more heavily toward GMO-free food.

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Some food companies are quietly dumping GMO ingredients