Some genetic engineering is focusing on ways to make unborn children have a certain eye or hair color. I personally think this is a total waste of time and money, not to mention completely shallow. This is taking away from individual, personalized beauty.
There is also the issue of using genetic information about a person to discriminate against them. For example, if an individual is known to have genetic markers that indicate they may develop disease (or WILL develop a disease, such as Huntington's), they may very well find their opportunities limited. For example, if there are two equally qualified candidates for a job, or to adopt a child, the person who has "normal" genes may be chosen over the person who has "abnormal" genes. Sometimes law and ethics have a hard time keeping up with the speed at which science advances.
I think, too, that the original, intended application of genetic research has been to correct serious genetic defects, whether in embryos or in independent, living creatures. (The idea of gene therapy, as I understand it, is not only concerned with replacing bad genetic material with good genetic material; there's also the idea of "turning off" or "turning on" genes.) The .gov information site given below certainly only mentions medical applications.
An interesting and unexpected application not in medicine but in anthropology/archaeology or family tree research has come from the intial mapping of the human genome (a process of studying huge numbers of samples of human DNA from around the world in order to understand more fully how human DNA works so that scientists and doctors can begin to experiment more fully with gene therapy). Today, scientists and lay people alike have been using the insights gained from the human genome project to better understand patterns of migration of people across hundreds of centuries. If you submit a sample of your DNA, for example, it can be checked for genetic markers that can show whether or not you have a specific ancestry. The ancestry.com site below talks about how the new knowledge about the human genome can be used to confirm or debunk oral histories (e.g. whether or not there truly is Native American ancestry in my family).
One of the challenges that have resulted from genetic research has been the manipulation of gene therapy. Essentially, this form of science calls for manipulating genes within the embryo to eliminate conditions that would manifest itself into the life of the child. Indeed, the positive side would be apparent. However, one of the objections is that it could help to create a setting where individual rights are denied, as individuals whose genes are manipulated would have no say in having their genes altered. This brings science closer to horrific eugenics experiments where individuals' and thus social genetic makeup is altered at the hands of an external force without any sort of consent or institutional control. This could be a use that was not originally intended.