This article does well to mention that many free applications, OS, and toolkits are available but it's important to note that even more important than the fact that you can read the source of Linux, MySQL, etc is that you are free to modify the software to suit your needs. Yes, you need to make your changes available but that's only if you distribute what you've derived from the previous components.
To the patent encumbrance issue, most if not all free software projects are interested in making sure their code does not infringe on any patents and will generally work to remove infringing code. So beware of the company that threatens that a product infringes but does not back it up with direct references to code. Thanks and enjoy free software!
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