Well it depends really, some Windows servers run on IIS and some on Apache which is open source and is also run on Linux servers.
Windows servers will allow you ASP / ASP.NET and Cold Fusion, Microsoft SQL 2005 and in some cases CGI with FastCGI support whereas Linux servers won't (unless they have specialised mods).
Linux on the other hand has some of its own benefits such as URL masking, custom throttle policy, custom cron jobs, password protected directories.
As mentioned however these things might differ from host-to-host.
Linux in general is more secure than Windows servers and if you don't do ASP I would strongly recommend you get yourself Linux/BSD hosting.
Yahoo! runs on several big BSD servers while the entire Google site is run on multiple desktop-sized pc's running Linux.
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