I tend to base Origin based on what ability started the character down their path, rather than what necessarily gave them their abilities. So my Mercs/Poison is Natural origin even though his Poison secondary is delivered via grenades and needle ammunition (well, I can imagine it is anyway) and was initially concocted by him. Why is he Natural then? Because he became a Villain through his natural-born talent for leadership and the military training he received earlier in life. The /Poison secondary is something he picked up consciously to support his other abilities.
My Thugs/Traps is a Tech origin because he only became ambitious and notable when he acquired a suit of powered armor, manifested in the form of Traps. Prior to that he would've been on par with one of the unupgraded Punks. The suit is what gave him the abilities and confidence to become a leader.
Then there's my Bots/Traps, who is a Science origin because he was genetically engineered to have a 'superior' brain, at least in matters of mathematics. It was a success and he's used those abilities to craft robots and technological marvels worthy of any supervillain (or hero, in this case). Sure, he'd be completely useless in a fight without his technology but he would've never built it in the first place without the scientific process that gave birth to him.
But Origins do tend to be a tricky thing and there can very easily be more than one origin that a character qualifies for.
Birth of a Villain Group (Arc ID 60573): Designed for villains level 1 - 10. Found a villainous organization on Mercy Island. Find a base, recruit some minions, gather valuable equipment, and destroy your enemies!
So, I found the Wiki on Marvel's Doctor Doom: http://en.wikipedia.org/wiki/Doctor_Doom
He's a scientist who scars his face in a lab experiment. He's got powered armor, and knows some magic he learned from Tibetan Monks. Plus, he's also used science to give himself some innate abilities. I'm inclined to go with Max's definition and call him "science origin".
I like to go off of what their DO's and SO's say, because that's the in game stuff that is going to make my origin choice feel more alive. If it's likely that my character would get more powerful by experiencing a "Genetic Alteration" for example then well.... that is a DO for Science or Mutation, so probably should choose one of those. If "Genetic Alteration"s are unlikely for my character, then probably science and mutant are origins I'd steer clear of. On the other hand Natural/Tech use "Gadgets", and clearly not all natural characters are dependent upon such things.
http://paragonwiki.com/wiki/Enhancement_Names
1. The poisons readily available to any member of society and the character's skill is in using the poisons effectively
2. The poisons are extracted from various plants and animals and the extraction process requires personal skill.
The overlap between Tech and Natural is higher than most of the other combinations (the closest is Magic/Natural) since Natural characters often use Gadgets (or magic items) and the question becomes at once point does the power provided by their gear outweigh their personal power.