Let me throw in my opinion.
A vast majority of the veggies are genetically engineered just like our chickens are genetically engineered. If you select certain plants or chickens to breed, then you are engineering which genes get to reproduce. I see nothing wrong in trying to improve my flock by selecting my best birds to breed and nothing wrong by selecting my best tomatoes to save seeds from. When someone says that something is genetically enginnered, be careful about what they actually mean. I watch the History and Discovery Channels and, boy, can they twist facts around to make them sound a lot worse than they actually are.
What worries me is when they splice genes and do things on that level. I'm in favor of the research to lead to a better understanding of how things work at that level, since that could lead to cures for a lot of diseases, but I am worried about what someone with less than ethical morals can do with that knowledge.
So, back to your original question, as others have said, most seeds have been selectively bred from wild plants all over the world. Many fruits are not that way however, since many fruit seeds do not breed true. (Some do, but not all.) A lot are hybrids, crosses of different varieties. Use apples as an example. Very few, if any, apples will self-pollinate. They need a different variety of apple for them to pollinate and set fruit. All apple varieties I'm aware of are grown by grafting or budding (a form of grafting) the parent stock onto another apple tree. For example, all Granny Smith apples are clones of the one original tree that made Granny Smith apples.