Biotechnology is a rather controversial issue, but it is also an issue with tremendous potential to help mankind. Yield increases, pest control, water use efficiency--all these are potential benefits of human interference in plant and animal genetics. Such activity creates concerns for potential problems, however; are altered plants safe for consumption? Will altering genetics cause enough benefits to outweigh the risk? Is it ethical to tamper with God's creation?
These questions are not going away any time soon. Many people are already trying to answer questions such as these, but they have very different answers. Some approach the subject from an atheistic view, justifying anything they do for science. Others answer from an environmentalist, pantheistic perspective, condemning anything that isn't "natural". What does the Bible say? What should we say as Christians, creationists, and agriculturalists?
GMO's that are made of different created kinds (which are nearly all, I think) make me uneasy, especially if they are for food. So little is known of DNA and how it works. A problem which affects development (like with a placenta) might not show up until the third generation! I think much more care should be taken. I thought one of the first applications of GMO's was yeast that manufactured human insulin. This application, I think, is worth the risk for the benefit. Glowfish for aquariums are not. If some disaster happens from GMO's, it would be totally inappropriate to blame God, because we are messing with the boundaries of his created kinds.
Mixing proteins from different kinds seems to be the biggest concern for biotechnology. Selective breeding of different plants and animals is not forbidden in Scripture; Genesis chapter thirty contains an account of Jacob using genetics in his favor. What is forbidden in the Mosaic law (along with gathering sticks on the Sabbath) is: "Thou shalt not sow thy vineyard with divers seeds: lest the fruit of thy seed which thou hast sown, and the fruit of thy vineyard, be defiled" (Deuteronomy 22:9).
I take this to be a spiritual analogy, as well as a precaution to prevent plant diseases. I don't really think it applies as more than advice today, but it is good advice for anyone without the effective means of controlling pests.
Wantonly mixing different kinds of plants, animals, and fungi for no good reason might not be specifically forbidden, but it seems a little risky at times. Like you pointed out, we don't exactly know everything about DNA yet, and it might take a while to discover problems. On the other hand, much of the research has more potential than apparent risk. Starvation is generally a much bigger risk than anything posed by GMOs.