Updated: April 11, 2015
Let me begin with an analogy, sort of. The fact Leonardo painted Mona Lisa with her mouth closed indicates she had bad teeth. This would be a very wrong summary to a nice work of art. Similarly, if we look at the relatively recent Howtogeek article of the dangers of free software, most notably the top ten downloads found on one of the popular software centrals, the same thing can be said about its ending. Not in line with an otherwise fairly good essay.
The conclusion is, paraphrasing, free software is dangerous, especially when the end product is you, ergo free. In other words, you get free goods, but the loaded malware, spyware, adware, and other crap that comes with the free stuff actually uses you to benefit advertisers and other companies. Ergo, not free. But this is not quite accurate, which is why I decided to write this response.
Note: Image taken from Wikimedia, licensed under CC BY-SA 3.0.
What's this all about?
Yes, indeed, Howtogeek went on and downloaded top 10 apps from Download.com, and then tested what happens when you install these without paying attention to all the little clicks during the installation process. The end result was, tons of spyware, adware, crapware, and other unwanted programs installed, clearly in violation of the promised Download.com service. Then, the author went on and concluded that everyone is bundling, and that there are no safe free software download sites, and that free software is risky, because the real product is you. So far so good.
Why this is not entirely accurate
Following this logic, pretty much any free product is potentially using the user. Google, Yahoo, Facebook, all the others, they use your data to earn money. And this is the case, actually. Perhaps the collection of data is done in a slightly different manner, and people do voluntarily give up lots of personal information about themselves, but in the end, the data is used for advertising, profiling and whatnot. For that matter, Howtogeek does have follow us buttons pointing to Google+, Facebook and Twitter, free services that also partake in milking the user's free will in return for money.
Yet, we are not all victims of fraud and phishing, not everyone's rights are being abused, and some of us do have browsers free of third-party addons. Not all is bad, and therefore there must some middle version of truth out there.
However, I do agree that bundled crap is totally annoying. A good example of this would be uTorrent, a free BitTorrent client that, once upon a time, managed to sneak in shit onto one of my boxes despite me not having done anything that would promote such fecal spreading. Now, does that mean all free BitTorrent clients sin the same sin? No. I did replace uTorrent, however not with any special payware software. Instead, I selected another free solution called qBittorent, which offers similar functionality without any third-party components.
Who is to blame?
All right. One, we have a problem, and we will discuss it. Two, I will give you actual advice how to continue enjoying free software without compromising your systems, otherwise this whole article would be pointless. But let's begin with the situation at hand. Bundled third-party shit.
The simple fact is, you get crap when you should not. From the legal perspective, it's all probably covered somewhere, somehow, so you can't really sue the download sites, or even the vendors offering these bundled packages. Somehow, it will be your fault, because you accepted the terms of use, and missed or ignored all the little fine print, checkboxes, and such. Truth to be told, you can install most of the top 10 software on Download.com without getting any extras, but it requires paying close attention to what you're doing.
But let's focus on the culprit. Who is to blame? After all, people need to earn money. The software business is not very profitable, and most websites offering content and/or product do not earn sufficient money to make a living. People expect all this marvelous stuff out there on the Web, but they forget that people making that stuff need to pay their bills, too.
In most cases, some gentle advertising can cover the hosting costs, server equipment, bandwidth, and maybe an odd part-time administrator, moderator, designer, or such to keep things tidy. The rest simply won't happen. Faced with a choice between shutting down their business or making extra money, most people will go for the second option. Alternatively, you will end up with honest people going out of business.
Donations do not work. Grace and good will do not work. And when people start charging money for their previously freely offered software, the community gets angry and whatnot. It's a paradox really. Just look at the reddit thread regarding Parted Magic going payware to survive. Then, people also ridicule the old new sites that still require subscriptions to serve content. Another paradox.
In the end, people equate the freedom of access to information to freedom of cost. In other words, the fact information is largely free on the Internet means also the services and products should be free. This is fine. But we cannot ignore the fact people producing things need to cover their costs, in some magical way. The fourth law of thermodynamics.
None of this exonerates leeches bundling shit with their stuff and peddling it to unsuspecting users. None of this really makes a difference to less skilled users suddenly having their browser homepage hijacked and redirected to some ultra shitty advertisement portal. But this does not mean that all free stuff is bad, and that there is only one way to make free less free without causing rebellion with the free-loving Internet users.
Therefore, the answer to our question, who to blame is, as follows. Given the need, a solution will come into existence to satisfy the need. Supply and demand. The reason that bundled third party crap exists in the first place is because it satisfies the monetary need of those bundling it. For a large part, most software companies are not criminals, and if they had the choice to earn the same kind of money in a more honorable way, they probably would. Faith in humanity and all that.
Or they might be greedy bastards. But wait. Everyone? Every single download site out there? Everyone? Do you really thing every CS graduate now working for SourceForge, Download.com, CNET, Softpedia, and other sites has come out of their class and went to work with the notion they will be scamming noobs with crappy software? Do you really think that the collective mind of people working in these companies is one of total moral abjection, depravity and pure greed? Yes, some must be assholes, some must be marketing asswipes, some might be managers who sniff their socks and like their presentations, but most just want to go home and pay their bills and continue their pointless living.
Solution
You CANNOT change the way the world works. The Internet will continue revolving around people demanding free stuff without any notion of gratitude or even a speck of background thought for people producing content. That's how it is. You cannot change it. And you should not worry about that.
What you CAN do is make sure you continue enjoying high-quality software, free or paid, without compromising your security and privacy. And there are several useful tips and tricks that can help you achieve that. To wit, this part of the article. How to get software and protect your e-virginity.
Where to look
What you need to do is search for reputable sites, which will teach you where to look for software, what products to choose and avoid, general tips, and such. It's a tricky thing, because you don't really know what sites to trust in the first place, right. Even those stumbling across Dedoimedo the first time might say, who the hell is this ranting loon, and why should I trust his opinion and recommendations? Indeed, that way the lunacy waits, so let's establish a few axioms. One, I'm always right, so listen to me.
Two, if you want great advice on free software, then your best portal is Gizmo's Freeware, also known as techsupportalert.com, which is entirely dedicated to this mission. Making your free software life wonderful. You might also like my Greatest sites list, as well as my recommended Windows and Linux software collections. Some of the entries are slightly outdated, but most of it is fine. And there, you'll get all the stuff you need. Fine. No drama. In fact, just use Gizmo and forget all the nonsense.
How to download & test
Let's say you did decide on several programs you want to try. There is a proper way of doing it. One, NEVER deploy new software on your important, production machines. Never. Always test on a separate, isolated host. This can also be a virtual machine, if you will. To wit, you might want to acquaint yourselves with some neat virtualization software.
Always test only one program at a time. And while doing that, you should also consider using imaging software, so that if something goes wrong, you can recover back to a previous, healthy state. Backups of your data also critical.
Try to download from official vendor sites
In those cases where the vendor provides download from their own servers, there's less chance of you landing on crap. Moreover, always pay close attention to what you are about to download, including alternative download options, fine print, and such. This is not a trivial task, and you should not treat it like an HR memo on recycling.
Use Linux
As weird as it sounds, using Linux reduces your chance of getting shit on your systems. The reasons are manyfold. As a platform, Linux is less likely to be flavored with feces, although Android-based vendors and companies are doing pretty well in changing that. While the application store concept works marvelously, with digitally signed repositories, many vigilant eyes checking and controlling the ingress of new software into the server database, and with a single source for software installations, in the mobile world, by design, you still get in-software ads and other annoying crap. Basically the same thing, and yet this is perfectly acceptable on mobile but not on desktops for some reason. But let's ignore this particular problem. Let's focus on the desktop.
So yes, you have software managers, which connect to the central Linux distribution repositories, and allow you to browse for content, including screenshots, reviews, and other useful information. All of this can be helpful in minimizing risks for exposure to brown matter. Open-source licensing also helps.
Advanced tip: Fake user agent
Modern browsers, like Firefox and Chrome support extensions, which can alter the basic behavior of the software. You can fake the identifier string called user agent that your browser sends whenever it requests pages from servers, and present themselves as something else entirely. This can lead to unexpected results in normal day-to-day browsing, but when you're hunting for new software, if your browsers tells the download server it's some obscure, weird product, the server may skip offering bundled crap. After all, almost the entire adware and malware ecospace revolves around Windows. If you're using something else, your world will be devoid of all this drama.
Advanced tip: Noscript
This little Firefox extension, and there are a bunch of similar addons for Chrome, blocks the execution of scripts on websites. It's convenient for security, but it has many other uses. It makes the Web quieter, cleaner, more peaceful, and on download sites, you often don't get to see the bundle offers, because these rely on properly identifying the visitor and offering the right kind of crap. Again, you might argue, why should it prowl these crap sites in the first place, but if you need to obtain a piece of software you like and want, and you can get it free of shit by using Noscript, then yes, by all means, do it.
Anti-virus software is pointless!
The author of the Howtogeek article also noticed that anti-virus programs ignored most if not all of it. Well, perhaps, because someone made an outstanding legal job. And because anti-virus software is useless. Here's another reason why you don't need it.
Conclusion
The Howtogeek article is a valuable, eye-opening piece of information. But it ends on a dramatic, unhelpful, blanket note. Free software is not the devil. Some of it is shit, but then paying money does not guarantee pristinity or satisfaction. If anything, the price has nothing to do with it, although money is the motivator behind the bundling. Your choice of programs for your operating system should be based on actual need and quality first and foremost.
Then comes the second part, obtaining the software in a safe manner. If you follow advice on various reputable sites, use a strict testing method combined with data backup and system imaging, you are probably going to be okay. Some advanced methods, including alternative operating systems, can help you gain an extra edge in this neverending battle between the forces of evil and good, I mean the Internet dramatics.
Last but not the least, if you like to reason, you might realize that the world of software is not a simple thing, and although most people are morons, not everyone writing code for living is a criminal in making, and you cannot abstractize their work into a single sentence. The only thing that is definite is that, there will always be someone trying to make a profit from you, be it in person or in the digital world. You may partake or not, but you DO have a choice.
Cheers.