Ethics

One big thing to think about is safety.  If recombinant organisms are turned loose in the wild the unintended consequences could be disasterous - so it is only wise to consider very carefully the possible ramifications of using recombinant organisms outside of the laboratory setting.

Herbicide resistant plants - suppose they cross pollinate the weeds, which then become herbicide resistant?

Bt toxin as insecticide - it's still an insecticide and potentially harmful to humans and disruptive to the food chain.

Would you want bacteria that could eat an oil slick off the ocean getting into a supertanker's hull?

Genetic screening for diseases - should your insurance company have access to this information? 

Cloning, embryonic stem cell research, immortality?  There are some people who think certain avenues of research shouldn't be embarked upon because of the potential problems awaiting us.