To me it comes back to three points:
1) If experts, handed a sample of a clearly changed organism, cannot determine whether that change was accomplished through laboratory DNA modification or through selective breeding, requiring labels for one but not the other makes no sense and is likely to mislead consumers.
2) If the problem isn't actually the laboratory nature of the changes, but the change itself, labeling laboratory-made changes is actively misleading. It gives people a scapegoat ("GMO") without addressing the real problem - tinkering with organisms for our own benefit.
3) If the problem isn't change, or laboratory change, but your dislike of business practices, and GMO labeling is just a way to strike back at corporate agribusiness, you really need to look at your choice of target. There is nothing inherently corporate agribusiness about GMO. Universities, non-profits, and individuals all have access to those techniques. It isn't common today because it is new, but eventually it will be no more "corporate" than yeast. See groups like:
Genspace
Personally, I'm skeptical about human-induced change/control. Humans consistently overestimate their ability to control other organisms (everything, really). However, I also think there is a first-world problem issue with this discussion. As wealthy (by world standards) 1st worlders we have the luxury of worrying about how a plant was modified. For people dying of malnutrition, people beset by drought and crop blights, the fact is that they need the food and the "maybe" risks you can cite for "GMO" really don't compare to the "happening right-the-bleep-now" risks they are dying from every day. Legitimizing "maybe" fears will result in more deaths from the "certainly" problems people face today.
If you accept that humans can/should change our domesticated plants and animals to deal with changing threats/needs (new insect/fungus traits, climate change, improved understanding of nutrition, etc.) then faster methods are better for mankind. Rather than having to wait 10 years for a blight-resistant strain to develop, while people are dying or suffering the effects of malnutrition, you can make the same change in a year and save lives. A win for mankind.
I know I'm bucking conventional wisdom but that's my take.