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fundamental difference between windows and linux are:
1. Full access vs. no access
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.

2. Licensing freedom vs. licensing restrictions
Along with access comes the difference between the licenses. Iâ??m sure that every IT professional could go on and on about licensing of PC software. But letâ??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 itâ??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 youâ??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 havenâ??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 canâ??t say one was more pleased than the other. This of course begs the question â??Why do so many say that Microsoft support is superior to Linux paid support?â??

4.Command line vs. no command line
No matter how far the Linux operating system has come and how amazing the desktop environment becomes, the command line will always be an invaluable tool for administration purposes. Nothing will ever replace my favorite text-based editor, ssh, and any given command-line tool. I canâ??t imagine administering a Linux machine without the command line. But for the end user â?? not so much. You could use a Linux machine for years and never touch the command line. Same with Windows. You can still use the command line with Windows, but not nearly to the extent as with Linux. And Microsoft tends to obfuscate the command prompt from users. Without going to Run and entering cmd (or command, or whichever it is these days), the user wonâ??t even know the command-line tool exists.

5.Flexibility vs. rigidity

compare Linux (especially the desktop) and Windows to a room where the floor and ceiling are either movable or not. With Linux, you have a room where the floor and ceiling can be raised or lowered, at will, as high or low as you want to make them. With Windows, that floor and ceiling are immovable. You canâ??t go further than Microsoft has deemed it necessary to go.

Take, for instance, the desktop. Unless you are willing to pay for and install a third-party application that can alter the desktop appearance, with Windows you are stuck with what Microsoft has declared is the ideal desktop for you. With Linux, you can pretty much make your desktop look and feel exactly how you want/need. You can have as much or as little on your desktop as you want. From simple flat Fluxbox to a full-blown 3D Compiz experience, the Linux desktop is as flexible an environment as there is on a computer.

Case Study - Windows XP vs. LINUX

Flavors
Both Windows and Linux come in many flavors. All the flavors of Windows come from Microsoft, the various distributions of Linux come from different companies (i.e. Linspire, Red Hat, SuSE, Ubuntu, Xandros, Knoppix, Slackware, Lycoris, etc. ).
Windows has two main lines. The older flavors are referred to as "Win9x" and consist of Windows 95, 98, 98SE and Me. The newer flavors are referred to as "NT class" and consist of Windows NT3, NT4, 2000, XP and Vista. Going back in time, Windows 3.x preceded Windows 95 by a few years.
The flavors of Linux are referred to as distributions (often shortened to "distros"). All the Linux distributions released around the same time frame will use the same kernel (the guts of the Operating System). They differ in the add-on software provided, GUI, install process, price, documentation and technical support. Both Linux and Windows come in desktop and server editions.

Cost
For desktop or home use, Linux is very cheap or free, Windows is expensive. For server use, Linux is very cheap compared to Windows. Microsoft allows a single copy of Windows to be used on only one computer. Starting with Windows XP, they use software to enforce this rule (Windows Product Activation at first, later Genuine Windows). In contrast, once you have purchased Linux, you can run it on any number of computers for no additional charge.

The upgrade edition of Windows XP Home Edition sells for about $100, XP Professional is about $200. The "full" version of XP Home is about $200, the full version of XP Professional is $300.

You can purchase assorted distributions of Linux in a box with a CD and manuals and technical support for around $40 to $80 (some distributions may be less, others may be more).

Graphical User Interface
Both Linux and Windows provide a GUI and a command line interface. The Windows GUI has changed from Windows 3.1 to Windows 95 (drastically) to Windows 2000 (slightly) to Windows XP (fairly large) and is slated to change again with the next version of Windows, the one that will replace XP. Windows XP has a themes feature that offers some customization of the look and feel of the GUI.
Linux typically provides two GUIs, KDE and Gnome. See a screen shot of Lycoris and Lindows in action from the Wal-Mart web site. The lynucs.org web site has examples of many substantially different Linux GUIs. Of the major Linux distributions, Lindows has made their user interface look more like Windows than the others.

Networking
They both do TCP/IP. Linux can do Windows networking, which means that a Linux computer can appear on a network of Windows computers and share its files and printers. Linux machines can participate on a Windows based network and vice versa.

Multiple Users
Linux is a multi-user system, Windows is not. That is, Windows is designed to be used by one person at a time. Databases running under Windows allow concurrent access by multiple users, but the Operating System itself is designed to deal with a single human being at a time. Linux, like all Unix variants, is designed to handle multiple concurrent users. Windows, of course, can run many programs concurrently, as can Linux. There is a multi-user version of Windows called Terminal Server but this is not the Windows pre-installed on personal computers.

File Systems
Windows uses FAT12, FAT16, FAT32 and/or NTFS with NTFS almost always being the best choice. The FATx file systems are older and have assorted limitations on file and partition size that make them problematical in the current environment. Linux also has a number of its own native file systems. The default file system for Linux used to be ext2, now it is typically ext3. Other supported file systems includes XFS, JFS, JFFS and Reiser3. Reiser4 is in development.

Shutting Down
Both have to be told to shut down and for the same reason, to quiesce in-flight activity in an orderly manner. You shut down Windows thru the Start button, then select Shutdown. In both the KDE and Gnome GUIs for Linux, you shut the system down by first logging out (equivalent to logging off in Windows). In Gnome, you select the Halt option, in KDE, the shutdown option. Linux can also be shut down from a command prompt using the shutdown command which can either shut the system down immediately or be told to shut it down at some time in the future. Windows XP also has a shutdown command, earlier versions of Windows did not

User Data
Windows allows programs to store user information (files and settings) anywhere. This makes it impossibly hard to backup user data files and settings and to switch to a new computer. In contrast, Linux stores all user data in the home directory making it much easier to migrate from an old computer to a new one. If home directories are segregated in their own partition, you can even upgrade from one version of Linux to another without having to migrate user data and settings.

I got this from written below link:-
Linux vs Windows (a comparison)
www.michaelhorowitz.com/Linux.vs.Windows.html

Case Study - Windows XP vs. LINUX

Flavors
Both Windows and Linux come in many flavors. All the flavors of Windows come from Microsoft, the various distributions of Linux come from different companies (i.e. Linspire, Red Hat, SuSE, Ubuntu, Xandros, Knoppix, Slackware, Lycoris, etc. ).
Windows has two main lines. The older flavors are referred to as "Win9x" and consist of Windows 95, 98, 98SE and Me. The newer flavors are referred to as "NT class" and consist of Windows NT3, NT4, 2000, XP and Vista. Going back in time, Windows 3.x preceded Windows 95 by a few years.
The flavors of Linux are referred to as distributions (often shortened to "distros"). All the Linux distributions released around the same time frame will use the same kernel (the guts of the Operating System). They differ in the add-on software provided, GUI, install process, price, documentation and technical support. Both Linux and Windows come in desktop and server editions.

Cost
For desktop or home use, Linux is very cheap or free, Windows is expensive. For server use, Linux is very cheap compared to Windows. Microsoft allows a single copy of Windows to be used on only one computer. Starting with Windows XP, they use software to enforce this rule (Windows Product Activation at first, later Genuine Windows). In contrast, once you have purchased Linux, you can run it on any number of computers for no additional charge.

The upgrade edition of Windows XP Home Edition sells for about $100, XP Professional is about $200. The "full" version of XP Home is about $200, the full version of XP Professional is $300.

You can purchase assorted distributions of Linux in a box with a CD and manuals and technical support for around $40 to $80 (some distributions may be less, others may be more).

Graphical User Interface
Both Linux and Windows provide a GUI and a command line interface. The Windows GUI has changed from Windows 3.1 to Windows 95 (drastically) to Windows 2000 (slightly) to Windows XP (fairly large) and is slated to change again with the next version of Windows, the one that will replace XP. Windows XP has a themes feature that offers some customization of the look and feel of the GUI.
Linux typically provides two GUIs, KDE and Gnome. See a screen shot of Lycoris and Lindows in action from the Wal-Mart web site. The lynucs.org web site has examples of many substantially different Linux GUIs. Of the major Linux distributions, Lindows has made their user interface look more like Windows than the others.

Networking
They both do TCP/IP. Linux can do Windows networking, which means that a Linux computer can appear on a network of Windows computers and share its files and printers. Linux machines can participate on a Windows based network and vice versa.

Multiple Users
Linux is a multi-user system, Windows is not. That is, Windows is designed to be used by one person at a time. Databases running under Windows allow concurrent access by multiple users, but the Operating System itself is designed to deal with a single human being at a time. Linux, like all Unix variants, is designed to handle multiple concurrent users. Windows, of course, can run many programs concurrently, as can Linux. There is a multi-user version of Windows called Terminal Server but this is not the Windows pre-installed on personal computers.

File Systems
Windows uses FAT12, FAT16, FAT32 and/or NTFS with NTFS almost always being the best choice. The FATx file systems are older and have assorted limitations on file and partition size that make them problematical in the current environment. Linux also has a number of its own native file systems. The default file system for Linux used to be ext2, now it is typically ext3. Other supported file systems includes XFS, JFS, JFFS and Reiser3. Reiser4 is in development.

Shutting Down
Both have to be told to shut down and for the same reason, to quiesce in-flight activity in an orderly manner. You shut down Windows thru the Start button, then select Shutdown. In both the KDE and Gnome GUIs for Linux, you shut the system down by first logging out (equivalent to logging off in Windows). In Gnome, you select the Halt option, in KDE, the shutdown option. Linux can also be shut down from a command prompt using the shutdown command which can either shut the system down immediately or be told to shut it down at some time in the future. Windows XP also has a shutdown command, earlier versions of Windows did not

User Data
Windows allows programs to store user information (files and settings) anywhere. This makes it impossibly hard to backup user data files and settings and to switch to a new computer. In contrast, Linux stores all user data in the home directory making it much easier to migrate from an old computer to a new one. If home directories are segregated in their own partition, you can even upgrade from one version of Linux to another without having to migrate user data and settings.

I got this from written below link:-
Linux vs Windows (a comparison)
www.michaelhorowitz.com/Linux.vs.Windows.html