At least from my perspective, the biggest talking point regarding GMOs is a sort of panic that mutant plants will take over the earth. While cross-contamination is a legitimate concern particularly impacting conventional and organic farmers, I believe it is second to a bigger issue.
If you're a long-time reader, you may be surprised that I am less up-in-arms over cross-contamination than you might expect. This past summer, I had the opportunity to discuss GMO crops with a scientist/attorney (rare combo) from a liberal non-profit. He made a valid point: natural selection favors only those traits which make a given species better suited for survival. With regard to GMO crops generally, however, one must take action for the "benefit" of the GMO plant to be conferred.
For example, Monsanto crops that are genetically modified to survive heavy dosages of herbicide (RoundUp Ready) only confer a benefit if and when the crops are sprayed with Monsanto. Thus, these plants are not better suited or more likely to survive in the wild than their non-GMO counterparts. Note that this is not the case with all genetically engineered plants. Take the GE eucalyptus created by ArboGen. Already considered an invasive species, the cold-tolerant GE eucalyptus has some serious environmental implications--particularly because these thirsty suckers minimize groundwater, rendering their environments highly flammable.
In sum, the issue of GMOs and cross-contamination warrants serious consideration (particularly when GMOs like the ArboGen eucalyptus may be released for a field trial without an appropriate Environmental Impact Statement)--but it's not my number one source of acid reflux.
My number one concern is that when a crop is engineered to be resistant to chemicals, farmers who normally use such chemicals sparingly and as needed are now incentivized to douse their crops in toxins; better to immerse your crops frequently than sparingly, risking crop failure. I think the Organic Consumers Association does a great job of underscoring the concern of herbicide abuse and rallying activists--but the organization really undermines its own legitimacy when it uses terminology like "merchant of death" to describe Monsanto. In this case, the facts speak for themselves.
GMOs are a tricky issue because different kinds of GMOs present different issues. It's difficult to inherently write them off as "good" or "bad." What we really need is a nuanced discussion and a flexible regulatory scheme. Don't hold your breath.