Then you would not be a very good search engine programmer.
First off, don't think of it as a binary "natural" vs. "unnatural", think of it as a continuous scale.
The HTML isn't the only place to look when it comes to this issue, in fact it is one of the worst places to look. A webgraph of the incoming and outgoing links is where you would start.
Where on the page is the link? It is pretty easy to pro grammatically recognize a a navigation sidebar or a footer.
How is the linking done? If all your links are to the home page with the same anchor text, and it is not the name of your site, but stuffed with keywords, it isn't hard to see how those might get discounted.
Are the links to your site on a site that is full of other suspicious links?
Are ALL your links reciprocal or three-way? Some reciprocal linking is natural, and occurs without being traded. But if all your links are reciprocal with other sites where all their links are reciprocal, things start to look bad.
All that was off the top of my head. Google has a lot of very smart people working on this full-time. You can still trick them, but don't assume that it is easy, or that it will keep working long-term.