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.

I don't know if there will ever be an objective measure of the ongoing care and feeding costs for Linux vs. Windows. If there were however, it would have to consider:

Dealing with bugs in the operating system 
Dealing with bugs in application software 
Dealing with viruses, worms, Spyware, etc.(big advantage to Linux here) 
Dealing with software upgrades to new versions (both the OS and applications)

Text Mode Interface

This is also known as a command interpreter.

Windows users sometimes call it a DOS prompt.

Linux users refer to it as a shell.

Each version of Windows has a single command interpreter, but the different flavors of Windows have different interpreters. In general, the command interpreters in the Windows 9x series are very similar to each other and the NT class versions of Windows (NT, 2000, XP) also have similar command interpreters. There are however differences between a Windows 9x command interpreter and one in an NT class flavor of Windows. Linux, like all versions of Unix, supports multiple command interpreters, but it usually uses one called BASH (Bourne Again Shell). Others are the Korn shell, the Bourne shell, ash and the C shell (pun, no doubt, intended).

GUI (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. 

Linux GUI is optional while the Windows GUI is an integral component of the OS.Expert says that speed, efficiency and reliability are all increased by running a server instance of Linux without a GUI, something that server versions of Windows can not do.They also says that detached nature of the Linux GUI makes remote control and remote administration of a Linux computer simpler and more natural than a Windows computer.

Flavors

Both Windows and Linux come in many flavour.

All the Flavours of Windows come from Microsoft and various distribution of Linux come from varios companies

i.e. Linspire, Red Hat, SuSE, Ubuntu, Xandros, Knoppix, Slackware, Lycoris,etc..

The flavour of Linux generally refferd to as distributions,all the linux distribution released around the same time will use the same kernal..

then the Question is arised..
How the Flavours are different??

Answer:: 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.

Both Linux and Windows come in desktop and server editions.

There may be too many distributions of Linux, it's possible that this is hurting Linux in the marketplace. IBM is a big Linux backer but does not have their own branded distribution. Currently there seem to be many nice things said about the Ubuntu distribution.

Linux is customizable in a way that Windows is not. For one, the user interface, while similar in concept, varies in detail from distribution to distribution. For example, the task bar may default to being on the top or the bottom. Also, there are many special purpose versions of Linux above and beyond the full blown distributions described above. For example, NASLite is a version of Linux that runs off a single floppy disk (since revised to also boot from a CD) and converts an old computer into a file server. This ultra small edition of Linux is capable of networking, file sharing and being a web server.