I'm going to use your examples
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"Humans have emotions - clearly not natural!" Chemical reactions in our brain react to stimuli, triggering hormones and reactions to stimulate our feelings, complex but natural indeed.
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Emotions clearly are natural. Humans did not manufacture them; they would exist without our intervention. However what would not be natural is the feeling you get when on LSD or any other substance for that matter. While some drugs are "natural" in the sense that they're made in plants or whatever, they are not "meant" to be taken by us. They disrupt the careful chemical balance that we as organisms maintain.
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"Humans make atomic bombs, surely these aren't natural?" Why not? When an atom is split, the natural reaction is a huge explosion. Not very nice, no, but still a natural process.
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But it is not a process that will occur on its own. An atom will not split under normal conditions. It is only our interference that causes it to split.
Now the reaction after the split is a natural reaction. But the split itself is not.
Anyway I guess my definition would be anything that can occur without our interference is a natural process. Fire is a completely natural construct. But an engine is a completely artificial construct. It uses natural laws and constructs to function, but the end result is something nature would not have ever made on its own.
Now with things like gay marriage, the definition is a little tougher. Some argue that we only evolved sex for procreation with genetic diversity. I would argue back saying that at done point the evolutionary goal changed. Like other animals with long gestation periods, humans stop procreating after a couple children, and instead they devote their time to rearing the few kids that they do have. It's only more primitive animals that have sex with everything that moves.
So with gay marriage one must ask - what is the purpose? It does occur in animals, so it is probably not a choice (for most anyway... I know of a couple people who seemed to "switch" out of the blue...). But is it intended by nature? Or is it the result of something going wrong during gestation? I personally am leaning towards the latter. But even if it is due to an error, homosexuals shouldn't be denied happiness IMO