The answer is: it depends on a lot of factors. In general, game mechanics can't be copyrighted beyond the actual text (they can be patented though, and terms can be trademarked). I could make a Mekton knock-off right now, as long as I wrote all of the rules myself and didn't use any text or artwork from the original books. I could use all of the mechanics - d10 + stat + skill, damage mechanic, etc. I might run into issues with the build system, because large swathes of it are tables and those might be considered the "expression of an idea" and not rules. Even so, I am totally free to take the basic idea of the build system (containers to put things in, effects-based systems, armor, etc.) as long as the rest of it is original. Legally I would be in the right. That doesn't mean that R. Talsorian Games couldn't try to stop it, and might have remedies to do so. Most retroclones follow this model, even to the point of adjusting experience point totals for level charts and changing the contents of other tables.
Also, it's been pointed out that many retroclones are done so under the auspices of the OGL, where the creators explicitly allow people to create works based on it (provided they do it properly). Other games, such as Fuzion, are not OGL (despite what the In.Fuzion creator claimed). That is certainly, legally and conceptually, the biggest difference between retroclones and other problematic games.
And I do have a fan adaptation of Tribe 8 (someone else's game) - to Fate Core (also someone else's game) right here in Google Drive. I wrote every word of it myself. It contains no copyrighted elements from either Tribe 8 or Fate Core, the one piece of artwork is used with expressed permission, and even at 40 pages or whatever isn't playable without either rulebook. It's purely supplementary material. It's kind of a bucket of bits and pieces that can be used to run the game in Fate Core. In my opinion, and to the best of my knowledge, it doesn't infringe on anyone else's intellectual property. I could very well be wrong, and DP9 could likely take my documents down with little more than a DMCA notice. But because of the vagaries of game copyright law, I'd only have to file some serial numbers off and put it right back up. Whether or not that would make me the douchebag in the situation would depend a lot on how on how I handled it.
What about other industries? I've mentioned the plethora of Alberto's Mexican restaurant knock-offs in Southern California before. Similar name, similar characters on their signs, similar color scheme, similar menus. Or take the story I read some years ago of a Russian laundry detergent brand that copied the product labeling of the "Other Brand" from their competitor's television commercials (basically, casting themselves as the other brand). Those are the same situation as retroclones vis-a-vis In.Fuzion, right?
The difference, to me at least, is that those other types of industries are highly competitive and often engage in a games of slap-fight marketing. There are boundaries set for how far they go - both legally and ethically - and those boundaries are understood by everyone involved. Within the tabletop gaming industry, those boundaries are different - and the Mykal Lakims, Tracey Alleys, and Nathan Robertsons of the world are ignorant (sometimes willfully so) of those boundaries. Whether they believe it's okay to market their own copies of a product line based on some interpretation of "Fair Use", or recycling an old campaign map (because, really, who's going to know?) or thinking that putting a lot of effort into editing and compiling someone else's work without their permission justifies selling it - all of that is overstepping boundaries. In some cases it may be legal, but the angry reaction by the designers and writers is justified nonetheless. This is because of their expectation for how the tabletop gaming industry works. Don't blatantly copy other people's stuff. Own your shit.
So, to me at least, that defines the difference between a retroclone and a blatant swipe of someone else's work. For anyone who is interested in more detailed discussion about copyright, trademarks, and patents - and what is likely acceptable or not acceptable - I found a really good thread about it on Boardgamegeek. It was highly informative about some details that even I really wasn't aware of, and tackles some of the most persistent myths about copyright. Be warned, it's at least a dozen pages long and meanders through a lot of different areas. It also contains links to a host of other interesting resources.