WINDOWS VS LINUX
#1.ull access vs. no access
Having access to the source code is probably the single most significant difference between Linux and Windows. The fact that Linux belongs to the GNU Public License ensures that users (of all sorts) can access (and alter) the code to the very kernel that serves as the foundation of the Linux operating system. You want to peer at the Windows code? Good luck. Unless you are a member of a very select (and elite, to many) group, you will never lay eyes on code making up the Windows operating system.
You can look at this from both sides of the fence. Some say giving the public access to the code opens the operating system (and the software that runs on top of it) to malicious developers who will take advantage of any weakness they find. Others say that having full access to the code helps bring about faster improvements and bug fixes to keep those malicious developers from being able to bring the system down. I have, on occasion, dipped into the code of one Linux application or another, and when all was said and done, was happy with the results. Could I have done that with a closed-source Windows application? No.
#2: Licensing freedom vs. licensing restrictions
Along with access comes the difference between the licenses. I'm sure that every IT professional could go on and on about licensing of PC software. But let's just look at the key aspect of the licenses (without getting into legalese). With a Linux GPL-licensed operating system, you are free to modify that software and use and even republish or sell it (so long as you make the code available). Also, with the GPL, you can download a single copy of a Linux distribution (or application) and install it on as many machines as you like. With the Microsoft license, you can do none of the above. You are bound to the number of licenses you purchase, so if you purchase 10 licenses, you can legally install that operating system (or application) on only 10 machines.
#3: Online peer support vs. paid help-desk support
This is one issue where most companies turn their backs on Linux. But it's really not necessary. With Linux, you have the support of a huge community via forums, online search, and plenty of dedicated Web sites. And of course, if you feel the need, you can purchase support contracts from some of the bigger Linux companies (Red Hat and Novell for instance).
However, when you use the peer support inherent in Linux, you do fall prey to time. You could have an issue with something, send out e-mail to a mailing list or post on a forum, and within 10 minutes be flooded with suggestions. Or these suggestions could take hours of days to come in. It seems all up to chance sometimes. Still, generally speaking, most problems with Linux have been encountered and documented. So chances are good you'll find your solution fairly quickly.
On the other side of the coin is support for Windows. Yes, you can go the same route with Microsoft and depend upon your peers for solutions. There are just as many help sites/lists/forums for Windows as there are for Linux. And you can purchase support from Microsoft itself. Most corporate higher-ups easily fall victim to the safety net that having a support contract brings. But most higher-ups haven't had to depend up on said support contract. Of the various people I know who have used either a Linux paid support contract or a Microsoft paid support contract, I can't say one was more pleased than the other. This of course begs the question "Why do so many say that Microsoft support is superior to Linux paid support?"

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