Windows and Linux often use two different web server applications. Windows sites use the Windows IIS server, while nearly all Linux sites use Apache.

Linux sites focus on PHP, Perl and other open-source script languages for server side scripting. Windows-based sites use ,NET and ASP technologies. They might also offer support for PHP.

Linux sites offer MySQL as the database for backend content storage. Windows sites will probably offer SQL Server, though some offer the Windows versions of MySQL as well.

There shouldn't be any difference between the two if you use strict web standards in your HTML. However, you need to be aware of the fact that, since Dreamweaver is a Windows-only product, it may insert some non-standard things into your HTML. Frontpage also does this.

When it comes to Web hosting, Linux has, for some time, been widely considered the best OS for Web servers. It's typically found to be the most reliable, stable and efficient system and, as such, it's commonly used for the demanding environment of Web and mail servers. If you use PHP, Perl or MySQL, Linux is the way forward. If apps are Microsoft-specific, then Windows is what you need.